GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Pseudomonas fluorescens FW300-N2E2

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate Pf6N2E2_373 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= SwissProt::Q5JEW1
         (445 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_373
          Length = 430

 Score =  283 bits (724), Expect = 8e-81
 Identities = 149/413 (36%), Positives = 236/413 (57%), Gaps = 16/413 (3%)

Query: 37  PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96
           P+VI+R +G  ++DVDG  + DF  G+GV+N+GH+HP+VV A++ Q +K +H       Y
Sbjct: 28  PLVIDRAQGSELWDVDGKRYLDFVGGIGVLNIGHNHPKVVAAVQAQLQKISHACFQVVAY 87

Query: 97  ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQ 156
           +  + LA++L E+  G    K  +  SGAEA E A+K+ +  T R   +AF   FHGRT 
Sbjct: 88  KPYLDLAQRLCEMIGGQHAYKAAFFTSGAEAVENAVKIARAHTNRSAVIAFRGGFHGRTL 147

Query: 157 AVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVF 216
              +LT      +  F P  P V H PYPN YR              +   L  ++E + 
Sbjct: 148 LGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGV-----------TSAMALQALDELLA 196

Query: 217 RHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFW 276
             V P  + AI  EP+QG+GG++  P  F + L+    ++GI+L  DE+Q G GRTGK++
Sbjct: 197 TQVAPERVAAIIIEPVQGDGGFLSAPAEFLQGLRALTQKHGIVLILDEIQTGFGRTGKWF 256

Query: 277 AIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEVV 335
             +H G++PDL+   K++ GGLPL+GV+ +A+I     PG    T+GGN ++ AA + V+
Sbjct: 257 GFQHAGIQPDLVTVAKSLAGGLPLSGVVGKAEIMDAPLPGGLGGTYGGNALSCAAALAVI 316

Query: 336 EIV--KELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPEL 393
           E    ++LL   + +G+ L + L   + +Y  IGD RG G   A+E++K  E +    +L
Sbjct: 317 EAYEQEQLLARGEVLGERLRQGLLHLQTRYPQIGDVRGSGFMLAIELIKHDEARTPDADL 376

Query: 394 RDRIVKESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEEALKAAL 444
             R++ E+   GL+++ CG   N +RF+ PL+ ++ +ID A++I + AL   L
Sbjct: 377 NQRLIDEARAGGLLVIKCGVYRNVLRFLAPLVTSEAQIDEALQILDGALARVL 429


Lambda     K      H
   0.320    0.141    0.418 

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: 485
Number of extensions: 30
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: 445
Length of database: 430
Length adjustment: 32
Effective length of query: 413
Effective length of database: 398
Effective search space:   164374
Effective search space used:   164374
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: 51 (24.3 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