GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuA in Pseudomonas fluorescens FW300-N1B4

Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate Pf1N1B4_4789 Butyryl-CoA dehydrogenase (EC 1.3.99.2)

Query= metacyc::MONOMER-11693
         (386 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4789 Butyryl-CoA
           dehydrogenase (EC 1.3.99.2)
          Length = 383

 Score =  256 bits (654), Expect = 8e-73
 Identities = 154/381 (40%), Positives = 224/381 (58%), Gaps = 5/381 (1%)

Query: 2   DHRLTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGG 61
           D  L+ E   +R    +FA   +AP    + +       +V +MG +GL G+  PEE+GG
Sbjct: 3   DIELSEEQVMIRDMARDFARGEIAPHAQAWEKAGWIDDGLVAKMGELGLLGMVVPEEWGG 62

Query: 62  MGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEILG 121
              DY+A  +A+EE++  D +    +    S+G  P+  +GT+ QK +WLP L SG+ +G
Sbjct: 63  TYVDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGTEEQKQQWLPDLASGQAIG 122

Query: 122 AFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKPD 181
            F LTEP  GS+A   RT A L +   +WVING K F++N       L  V AVT  +  
Sbjct: 123 CFCLTEPQAGSEAHNLRTRAELRDG--QWVINGAKQFVSNGKR--AKLAIVFAVTDPEL- 177

Query: 182 GKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQFL 241
           GK  IS+ +VP+ T GF V     K+G  ASDT  ++  +  VP ANLLGE+G+G A  L
Sbjct: 178 GKRGISAFLVPTETAGFIVDRSEHKMGIRASDTCAVTLNNCTVPEANLLGERGKGLAIAL 237

Query: 242 RILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMAR 301
             L+ GRI I+A A G+A+   + ++ YA +R  F + I  +Q+I   +ADM  + + AR
Sbjct: 238 SNLEGGRIGIAAQALGIARAAFEAALAYARDRVQFDKPIIEHQSIANMLADMHTRLNAAR 297

Query: 302 VGWRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRDS 361
           +    AA    AG+P   EA+ AKL++S +A      A QIHGGYG++ +YPV R +RD+
Sbjct: 298 LLILHAARLRSAGKPCLSEASQAKLFASEMAEKVCSSAIQIHGGYGYLEDYPVERYYRDA 357

Query: 362 KILEIGEGTSEVQRMLIAREL 382
           +I +I EG+SE+QRM+IAREL
Sbjct: 358 RITQIYEGSSEIQRMVIAREL 378


Lambda     K      H
   0.318    0.136    0.402 

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: 388
Number of extensions: 18
Number of successful extensions: 3
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: 386
Length of database: 383
Length adjustment: 30
Effective length of query: 356
Effective length of database: 353
Effective search space:   125668
Effective search space used:   125668
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.

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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, 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