GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Azospirillum brasilense Sp245

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate AZOBR_RS19590 AZOBR_RS19590 ornithine-oxoacid aminotransferase

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__azobra:AZOBR_RS19590
          Length = 405

 Score =  247 bits (631), Expect = 4e-70
 Identities = 147/371 (39%), Positives = 211/371 (56%), Gaps = 19/371 (5%)

Query: 78  DTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALT 137
           DT+G  ++DCL  +   N GH +P ++ A+  Q +K  L S+   +   A+  + LAALT
Sbjct: 37  DTEGNRYLDCLSAYSAVNQGHCHPKILEAMVQQASKLTLTSRAFRNDQLALFYEELAALT 96

Query: 138 PGKLKYSFFCNSGTESVEAALKLAKAYQS-----PRGKFTFIATSGAFHGKSLGALSATA 192
            G  K     NSG E+VE+A+K  + +       P  +   I  S  FHG+++  +S + 
Sbjct: 97  -GSHKI-LPMNSGAEAVESAIKTVRKWGYEVRGVPENQAEIIVCSDNFHGRTISIVSFST 154

Query: 193 KSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPG 252
               R  F P  PGFR VPFG+  A+  AL        +  AV+LEPIQGE GV++PP G
Sbjct: 155 DPDARGGFGPFTPGFRTVPFGDAAALEAALTP------NTVAVLLEPIQGEAGVVIPPAG 208

Query: 253 YLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGAT 312
           YL  VR LC E   +MILDE+QTG+GRTGK+ A EHE V+ D+  + KAL GG  P+ A 
Sbjct: 209 YLRRVRDLCTERNVVMILDEIQTGLGRTGKLLAEEHEGVEADVTLIGKALSGGFYPVSAV 268

Query: 313 IATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQ 372
           ++  EV  VL   P  H +TFGGNPLACA A A + VL+E+ +   A  +G   L+   Q
Sbjct: 269 LSNSEVLGVL--KPGQHGSTFGGNPLACAVARAAMRVLVEEGMIDNAAAQGAYFLE---Q 323

Query: 373 LAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPLT 432
           L     ++++EARG+G+++A+E      G     E  R R ++A   ++  TIRI PPL 
Sbjct: 324 LGAIRSNVIREARGRGLMLAVELHPEAGGARRYCEALRARGVLAKDTHD-HTIRIAPPLV 382

Query: 433 LTIEQCELVIK 443
           +T EQ +  ++
Sbjct: 383 ITREQVDWALE 393


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: 435
Number of extensions: 27
Number of successful extensions: 8
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: 405
Length adjustment: 32
Effective length of query: 427
Effective length of database: 373
Effective search space:   159271
Effective search space used:   159271
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