GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patA in Acidovorax sp. GW101-3H11

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate Ac3H11_1332 Acetylornithine aminotransferase (EC 2.6.1.11)

Query= BRENDA::P42588
         (459 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1332 Acetylornithine
           aminotransferase (EC 2.6.1.11)
          Length = 398

 Score =  222 bits (566), Expect = 1e-62
 Identities = 148/370 (40%), Positives = 203/370 (54%), Gaps = 22/370 (5%)

Query: 78  DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALT 137
           D  G+E+ID LGG  +  +GH +  +V A+Q+Q+AK    S     PL+  LA  L  L+
Sbjct: 33  DVNGKEYIDGLGGIAVNTLGHNHGKLVPALQDQIAKLIHTSNYYHVPLQEKLATKLVELS 92

Query: 138 PGKLKYSFFCNSGTESVEAALKLAKAYQSPRG--KFTFIATSGAFHGKSLGALSATAKST 195
              ++  FFCNSG E+ EAALK+A+ +   +G  K   +    AFHG+S+  +SAT    
Sbjct: 93  G--MQNVFFCNSGLEANEAALKIARKFGVDKGIAKPEIVVYEKAFHGRSIATMSATGNPK 150

Query: 196 FRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYLT 255
               F PL+ GF  VP  +IEA++ A     +   +V AV  E IQGEGG+      YL 
Sbjct: 151 IHNGFGPLVEGFVRVPMNDIEAIKQAT----EGNPNVVAVFFETIQGEGGINGMRIEYLQ 206

Query: 256 AVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIAT 315
            +RKLCDE G LM++DEVQ GMGRTGK FA +   + PD++ LAK LG GV PIGA +A 
Sbjct: 207 QLRKLCDERGWLMMIDEVQCGMGRTGKWFAHQWAGIVPDVMPLAKGLGSGV-PIGAVVAG 265

Query: 316 EEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLAR 375
            +  +VL   P  H TTFGGNPLA  A + TI ++ E  L   A Q GD L    ++   
Sbjct: 266 PKAANVL--QPGNHGTTFGGNPLAMRAGVETIRIMEEDGLLHNAAQVGDHLRAALQRELG 323

Query: 376 EYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNA---KTIRIEPPLT 432
             P  V+E RG+G+++ IE        N        R   AG L +      IR+ PPL 
Sbjct: 324 SLPG-VKEIRGQGLMLGIEL-------NKPCGALIGRAAEAGLLLSVTADSVIRLVPPLI 375

Query: 433 LTIEQCELVI 442
           LT  + + ++
Sbjct: 376 LTTAEADAIV 385


Lambda     K      H
   0.320    0.135    0.393 

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: 429
Number of extensions: 20
Number of successful extensions: 7
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: 459
Length of database: 398
Length adjustment: 32
Effective length of query: 427
Effective length of database: 366
Effective search space:   156282
Effective search space used:   156282
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 (21.8 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 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