GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1619
          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 (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