GapMind for catabolism of small carbon sources

 

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

Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate PfGW456L13_2494 Butyryl-CoA dehydrogenase (EC 1.3.99.2)

Query= metacyc::MONOMER-20677
         (380 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2494
          Length = 390

 Score =  192 bits (488), Expect = 1e-53
 Identities = 132/385 (34%), Positives = 187/385 (48%), Gaps = 12/385 (3%)

Query: 1   MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLL-GLPFSE 59
           M+F  S+EQ +++ S EG L    D  + +     + G+  A+W +  ++     +   E
Sbjct: 1   MEFAFSDEQEMIRASAEGFLADVSDSAAVRAAMVSERGFDEALWQRLCQEMYWPAIHIPE 60

Query: 60  EDGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGSK 119
             GG G G VE  I++E +G  L+  P+  T  +    L  A +  QK   LP I DGS 
Sbjct: 61  TYGGLGLGFVELTILLEQMGRRLLCSPFFATACMATPALLLAANDQQKQRWLPSIADGSV 120

Query: 120 TFAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDR 179
           T   A    N  W   DV  T    GDG+V+DG    VL+G  AD LI+ AR  G   ++
Sbjct: 121 TATLAFSSANG-WSADDVQATVVAEGDGYVLDGTLKHVLDGHGADLLIIAARQPGTTGEK 179

Query: 180 TGVGVFLVPADAKGITRKGYPTQDGLHA-ADITFTGVQVGADAAIGDPENALELIEAVVD 238
            G+ +F + A+  GI R+  PT D     A I   G+ + AD  +G+  N    +E V+ 
Sbjct: 180 -GISLFAMSAERAGIERQMLPTMDQTRRQARIQLKGLYLEADCLLGEFGNGWSHLERVLQ 238

Query: 239 DARTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAM 298
            A   L AE  G   + L  +V Y++ R+QFG PI SFQ L+HRAADM +  E ARS + 
Sbjct: 239 LACIGLAAEQTGGAQQVLDLSVAYMQERQQFGRPIASFQALKHRAADMMLQVECARSASY 298

Query: 299 FATMAAEF--------DDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIG 350
           +A   A+           A E   A A AK Q  ++      +SIQLHGG+G T E    
Sbjct: 299 YAACVAQEVLDPQGDPQVAAELPLAAALAKAQCSETYFSCASESIQLHGGVGFTWEYDPH 358

Query: 351 HYFKRLTMIEQTFGDTDHHLARVSA 375
            YFKR    E   G    H  R+++
Sbjct: 359 LYFKRARASESFLGLPAWHRERIAS 383


Lambda     K      H
   0.318    0.135    0.388 

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: 358
Number of extensions: 19
Number of successful extensions: 5
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: 380
Length of database: 390
Length adjustment: 30
Effective length of query: 350
Effective length of database: 360
Effective search space:   126000
Effective search space used:   126000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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