GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astC in Pseudomonas fluorescens FW300-N2C3

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate AO356_26715 AO356_26715 4-aminobutyrate aminotransferase

Query= reanno::Marino:GFF3099
         (404 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26715 AO356_26715
           4-aminobutyrate aminotransferase
          Length = 430

 Score =  219 bits (558), Expect = 1e-61
 Identities = 127/402 (31%), Positives = 221/402 (54%), Gaps = 33/402 (8%)

Query: 28  RGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLS-NVMTNEPALR 86
           R +G+ +WD +G  ++D  GGI V  +GH+HP +V A+  Q +K+ H    V+  +P L 
Sbjct: 33  RAQGAEVWDVDGARYLDFVGGIGVLNIGHNHPKVVAAVQAQLQKVSHACFQVVAYKPYLD 92

Query: 87  LAKTLCDLTFAERVFFA---NSGAEANEAAFKLARRYAWEHHGKEKNEIISFKNSFHGRT 143
           L K LC+L   ++ + A    SGAEA E A K+AR +        +  +ISF+  FHGRT
Sbjct: 93  LVKRLCELVGGQQAYKAALFTSGAEAVENAVKIARAHT------NRPAVISFRGGFHGRT 146

Query: 144 LFTVSVGGQPK-YLEGFEPAPGGIHHAEFND----------LESVKKL----ISKEKTCA 188
           L   ++ G  + Y + F P    + H  + +          L+++ +L    ++ ++  A
Sbjct: 147 LLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGFSSEMALQALNELLATQVAPDRVAA 206

Query: 189 IVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAYQMYGVVPD 248
           I++EP+QG+GG +     FLQ LR L +++  +L+ DE+Q+G GR+G ++ +Q  G+ PD
Sbjct: 207 IIIEPVQGDGGFLSAPPEFLQALRTLTEQHGIVLILDEIQTGFGRTGKWFGFQHAGIQPD 266

Query: 249 ILSSAKGLGGGFPVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVDTVSQPEILK 308
           +++ AK L GG P++ ++  A +  +   G  G TYGGNAL+CA A  V+D   Q ++L+
Sbjct: 267 LVTVAKSLAGGLPISGVVGRAHIMDAPLPGGLGGTYGGNALSCAAALAVIDAYEQEQLLE 326

Query: 309 GVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQGKAKD------FLNAGLE 362
             +   ++LR+G++ +  R+    +VRG G +L   L +  + ++ D       ++    
Sbjct: 327 RGQVLGERLRQGLLRLQARHPRIGDVRGTGFMLAIELIKDDEARSPDAELTQQLIDQARV 386

Query: 363 EGVMVLVAGA--NVIRLAPSLIIPEPDIELALERFEAAVKKL 402
             ++V+  G   NV+R    L+  E  I+ AL   EAA+ ++
Sbjct: 387 GRLLVIKCGVHRNVLRFLAPLVTEESQIDEALTILEAALLRV 428


Lambda     K      H
   0.318    0.137    0.406 

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: 450
Number of extensions: 20
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: 404
Length of database: 430
Length adjustment: 31
Effective length of query: 373
Effective length of database: 399
Effective search space:   148827
Effective search space used:   148827
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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