GapMind for catabolism of small carbon sources

 

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

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate PfGW456L13_1619 Medium-chain-fatty-acid--CoA ligase (EC 6.2.1.-)

Query= BRENDA::A4YDR9
         (549 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1619
           Medium-chain-fatty-acid--CoA ligase (EC 6.2.1.-)
          Length = 560

 Score =  224 bits (572), Expect = 5e-63
 Identities = 158/532 (29%), Positives = 256/532 (48%), Gaps = 23/532 (4%)

Query: 24  PLLF--LERAGKYFKDKTAVVYRDS-RYTYSTFYDNVMVQASALMRRGFSREDKLSFISR 80
           PLL   L  +G  ++    ++YRD  RY+Y T  + V   A+ L   G    D +  +  
Sbjct: 17  PLLIKRLLMSGARYEKTREIIYRDKLRYSYPTLIERVARLANVLTAAGVKPGDAVGVMDW 76

Query: 81  NRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQI 140
           +   +LE  F +P  G V+  IN RLSP+++ Y +NH++ +FV+V+  ++     ++ Q+
Sbjct: 77  DSHRYLECMFAIPMIGAVIHTINVRLSPEQILYTMNHAEDRFVLVNSEFVGLYKAIEGQL 136

Query: 141 KA--EIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTSGT 198
               + +LL D    +A       +   Y +L+   S         +E S+ T +YT+GT
Sbjct: 137 TTVDKTLLLTDLPEKTAD---LPNLVGEYEQLLAAASPQ-YDFEDFDENSVATTFYTTGT 192

Query: 199 TGLPKGVMHHHRGAFLNAMA-EVLEHQMD------LNSVYLWTLPMFHAASWGFSWATVA 251
           TG PKGV   HR   L+ M    +   +D       N VY+   PMFH  +WG  +    
Sbjct: 193 TGNPKGVYFTHRQLVLHTMGVSTIMGAIDSVRLLGTNDVYMPITPMFHVHAWGLPYVATM 252

Query: 252 VGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAGA 311
           +G   V   + D   +  L  KE+VT     PT+   + +      + F     +++ G+
Sbjct: 253 LGLKQVYPGRYDPEYLVELWRKEKVTFSHCVPTILQMVLNAKAAQTVDFGGW-KIVIGGS 311

Query: 312 APAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYVS 371
           A      +A +  G  +   YG++ET    S      E  +   +E+   + + G+P   
Sbjct: 312 ALNRTLYEAAKAKGIQLTAAYGMSETGPLVSCAHLNDELMAGTEDERTTYRIKAGVPGPL 371

Query: 372 FEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVVHP 431
            E  + D+ G  +P DG+T GE+V+R   +  GY+  P+K AE +  GW H+GD A +  
Sbjct: 372 VEAAIVDSEGNFLPADGETQGELVLRAPWLTEGYFNEPQKGAELWAGGWLHTGDVATLDS 431

Query: 432 DGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQ 491
            G I+I DR KD+I TGGE +SS+ +E  +     V+ VAV G PD +WGE   A + L+
Sbjct: 432 MGVIDIRDRIKDVIKTGGEWISSLDLEDLISRHAAVREVAVVGIPDPQWGERPFALLVLR 491

Query: 492 EGVKLTEEEVIKFCKE-----RLAHFECP-KIVEFGPIPMTATGKMQKYVLR 537
           EG  +   E+ +  K       L+ +  P +I     IP T+ GK+ K  +R
Sbjct: 492 EGHAIGARELKEHLKPFVELGHLSKWAIPSQIALVTEIPKTSVGKLDKKRIR 543


Lambda     K      H
   0.319    0.136    0.411 

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: 739
Number of extensions: 37
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: 549
Length of database: 560
Length adjustment: 36
Effective length of query: 513
Effective length of database: 524
Effective search space:   268812
Effective search space used:   268812
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