GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1332
          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:

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