GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Pseudomonas fluorescens FW300-N2E3

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate AO353_03315 AO353_03315 long-chain fatty acid--CoA ligase

Query= metacyc::MONOMER-20125
         (556 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_03315 AO353_03315 long-chain
           fatty acid--CoA ligase
          Length = 562

 Score =  138 bits (348), Expect = 5e-37
 Identities = 109/374 (29%), Positives = 176/374 (47%), Gaps = 36/374 (9%)

Query: 185 DPMILNYTSGTTSSPKGVVHCHRGIFIMTVDS---LIDWGVPKQP-------VYLWTLPM 234
           D  +L YT GTT   KG +  H  +      +   L  +G   +P       V +  LP+
Sbjct: 208 DVAVLQYTGGTTGLAKGAMLTHGNLVANMQQARACLGQFGSDGKPLLREGQEVMIAPLPL 267

Query: 235 FHANGWSYPWGMAAVGGTNICLRKFDSEI--IYDMIKRHGVTHMCGAPVVLNMLSNAPGS 292
           +H   ++       V G +  L     +I      +K    + + G   +   L + P  
Sbjct: 268 YHIYAFTANCMCMMVTGNHNVLITNPRDIAGFIKELKNWRFSALLGLNTLFVALMDHPNF 327

Query: 293 EPLKTTVQIMT--AGAPPPSAVLFRTESL-GFAVSHGYGLTETAGLVVSCAWKKEWNHLP 349
           + L  +   +T   G     A   R E + G  ++ GYGLTET+   V+C         P
Sbjct: 328 KTLDFSSLKLTNSGGTALVKATAERWEQITGCRITEGYGLTETSP--VACT-------NP 378

Query: 350 ATERARLKSRQGVGTV-MQTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEG 408
             +++R      +GTV +      +  +    V++     GE+ ++G  +M GY + PE 
Sbjct: 379 YGDKSR------IGTVGLPVPGTTLKVINDDGVEQPLGERGELCIKGPQIMKGYWQKPEA 432

Query: 409 TAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEA 468
           TA+ + ADGWF +GD+ V+ PDG++ I DR KD+II  G N+   E+E ++ +HP +   
Sbjct: 433 TAEVLDADGWFKSGDIAVIDPDGFVRIVDRKKDMIIVSGFNVYPNEIEDVVMAHPKVANC 492

Query: 469 AVVARPDEFWGETPCAFVSLKK-GLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKT 527
           AV+  PDE  GE    FV  ++ G++     +E+  YC+     Y VPK +V +E LP T
Sbjct: 493 AVIGVPDERSGEAVKLFVVAREAGISL----EELKAYCKENFTAYKVPKHIVLRESLPMT 548

Query: 528 STGKVQKFILRDMA 541
             GK+ +  LRD+A
Sbjct: 549 PVGKILRRELRDIA 562


Lambda     K      H
   0.319    0.135    0.412 

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: 752
Number of extensions: 45
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 556
Length of database: 562
Length adjustment: 36
Effective length of query: 520
Effective length of database: 526
Effective search space:   273520
Effective search space used:   273520
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 (21.7 bits)
S2: 53 (25.0 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