GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Pseudomonas fluorescens FW300-N2C3

Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate AO356_26365 AO356_26365 acyl-CoA dehydrogenase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_26365
          Length = 383

 Score =  257 bits (657), Expect = 3e-73
 Identities = 155/381 (40%), Positives = 221/381 (58%), Gaps = 5/381 (1%)

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

Query: 62  MGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEILG 121
              DY+A  +A+EE++  D +    +    S+G  P+  FGTD QK  WL  L SG+ +G
Sbjct: 63  TYVDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNFGTDEQKQTWLAELASGQAIG 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+ TPGF V     K+G  ASDT  ++ ++  VP ANLLG +G+G A  L
Sbjct: 178 GKKGISAFLVPTDTPGFIVDRTEHKMGIRASDTCAVTLSNCTVPEANLLGARGKGLAIAL 237

Query: 242 RILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMAR 301
             L+ GRI I+A A G+A+   + ++ YA +R  F + I  +Q+I   +ADM  + +  R
Sbjct: 238 SNLEGGRIGIAAQALGIARAAFEAALAYARDRVQFDKPIIEHQSIANLLADMHTRINATR 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: 395
Number of extensions: 22
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 (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