GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Pseudomonas putida KT2440

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate PP_4481 PP_4481 Succinylornithine transaminase/acetylornithine aminotransferase

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__Putida:PP_4481
          Length = 406

 Score =  201 bits (510), Expect = 5e-56
 Identities = 124/319 (38%), Positives = 175/319 (54%), Gaps = 19/319 (5%)

Query: 78  DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELL--DPLRAMLAKTLAA 135
           D  G+E ID  GG  +  +GH +P +V A+  Q A    H   +   +P   +  K + A
Sbjct: 38  DQSGRELIDFAGGIAVNALGHCHPALVKALTEQ-ANTLWHVSNVFTNEPALRLAHKLVDA 96

Query: 136 LTPGKLKYSFFCNSGTESVEAALKLAKAYQSPR---GKFTFIATSGAFHGKSLGALSATA 192
               +   +FFCNSG ES EAA KLA+     R    K   IAT  +FHG++L  +S   
Sbjct: 97  TFADR---AFFCNSGAESNEAAFKLARRVAHDRFGPQKHEIIATVNSFHGRTLFTVSVGG 153

Query: 193 KSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPG 252
           +  +   F P + G  HVP+ ++EA++  ++      D   AV++EPIQGE GV+     
Sbjct: 154 QPKYSDGFGPKITGISHVPYNDLEALKAQIS------DKTCAVVIEPIQGESGVVPADKA 207

Query: 253 YLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGAT 312
           YL   RKLCDE  AL+I DEVQTG+GRTG ++A +H  V PDIL  AK+LGGG  PIGA 
Sbjct: 208 YLEGARKLCDEHNALLIFDEVQTGVGRTGSLYAYQHYGVIPDILTSAKSLGGG-FPIGAM 266

Query: 313 IATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQ 372
           + T E+   L      H TT+GGNPL CA A A ++V+      A  + K +       Q
Sbjct: 267 LTTTELAKHLAVG--THGTTYGGNPLGCAVACAVLDVVNTPETLAGIKAKHERFKTRLEQ 324

Query: 373 LAREYPDLVQEARGKGMLM 391
           + ++Y +L  + RG G+L+
Sbjct: 325 IGQQY-NLFSQVRGVGLLL 342


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: 371
Number of extensions: 17
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: 459
Length of database: 406
Length adjustment: 32
Effective length of query: 427
Effective length of database: 374
Effective search space:   159698
Effective search space used:   159698
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