GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patA in Pseudomonas fluorescens GW456-L13

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate PfGW456L13_2301 Pyoverdin biosynthesis protein PvdH, L-2,4-diaminobutyrate:2-oxoglutarate aminotransferase (EC 2.6.1.76)

Query= BRENDA::P42588
         (459 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2301 Pyoverdin
           biosynthesis protein PvdH,
           L-2,4-diaminobutyrate:2-oxoglutarate aminotransferase
           (EC 2.6.1.76)
          Length = 466

 Score =  202 bits (515), Expect = 1e-56
 Identities = 138/412 (33%), Positives = 214/412 (51%), Gaps = 47/412 (11%)

Query: 78  DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQ-PLHSQELLDPLRAMLAKTLAAL 136
           D +G+ FIDCL G G   +GH +PVV+ A+Q  LA + PLH+ +L  P++    + L  L
Sbjct: 59  DVEGRTFIDCLAGAGTLALGHNHPVVIEAIQQVLADELPLHTLDLTTPVKDRFVQDLFGL 118

Query: 137 TPGKL----KYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATA 192
            P  L    K  F   +GT++VEAALKL +   +  G+ T I+  G +HG S GALS   
Sbjct: 119 LPPALAAEAKIQFCGPTGTDAVEAALKLVR---TATGRSTVISFQGGYHGMSQGALSLMG 175

Query: 193 KSTFRKP----------FMPLLPGFRHVPFG---------NIEAMRTALNECKKTGDDVA 233
               +KP          FMP    +R  PFG         N+  +   LN+ +      A
Sbjct: 176 SLGPKKPLGALLGSGVQFMPYPYDYR-CPFGLGGAQGVKANLSYLENLLNDPEAGVQLPA 234

Query: 234 AVILEPIQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQP 293
           AVI+E +QGEGGVI     +L  VR++ ++ G  +I+DE+Q+G  RTGKMFA EH  + P
Sbjct: 235 AVIVEVVQGEGGVIPADLDWLRGVRRITEQAGVALIVDEIQSGFARTGKMFAFEHAGIIP 294

Query: 294 DILCLAKALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQ 353
           D++ ++KA+GG  +P+   +  + + + L   P  H  TF GN +A AA  A +  L+E 
Sbjct: 295 DVVVMSKAIGGS-LPLAVVVYRDWLDTWL---PGAHAGTFRGNQMAMAAGCAVMRYLVEH 350

Query: 354 NLPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVD---------NEIGYNF 404
            +   A   G+ L +  R L R++P L  + RG+G+++ +E VD         +   +  
Sbjct: 351 KVCEHAAAMGERLAEHLRILQRDFPQL-GDIRGRGLMLGVELVDPTGALDAQGHPPAFAR 409

Query: 405 ASEMFRQRVLVAGTL-----NNAKTIRIEPPLTLTIEQCELVIKAARKALAA 451
            + + ++  L  G +      +   +R  PPL +T  Q + V +   +ALAA
Sbjct: 410 LAPLVQRECLKRGLILELGGRHGAVVRFLPPLVITAAQIDRVAEIFGRALAA 461


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: 508
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: 459
Length of database: 466
Length adjustment: 33
Effective length of query: 426
Effective length of database: 433
Effective search space:   184458
Effective search space used:   184458
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 preprint 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