GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2301
          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:

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