GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas fluorescens GW456-L13

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate PfGW456L13_1910 Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1910
          Length = 562

 Score =  137 bits (346), Expect = 8e-37
 Identities = 108/373 (28%), Positives = 175/373 (46%), Gaps = 34/373 (9%)

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

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

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

Query: 350 ATERARLKSRQGVGTV-MQTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEG 408
             +++R      +GTV +      +  +    V++     GE+ ++G  +M GY + P+ 
Sbjct: 379 YGDQSR------IGTVGLPVPGTTLKVINDDGVEQPLGERGELCIKGPQIMKGYWQKPDA 432

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

Query: 469 AVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTS 528
           AV+  PDE  GE    FV  ++      + +E+  YC+     Y VPK +V +E LP T 
Sbjct: 493 AVIGVPDERSGEAVKLFVVAREA---GVSLEELKAYCKENFTAYKVPKHIVLRESLPMTP 549

Query: 529 TGKVQKFILRDMA 541
            GK+ +  LRD+A
Sbjct: 550 VGKILRRELRDIA 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: 758
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 (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:

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