GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Pedobacter sp. GW460-11-11-14-LB5

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate CA265_RS15205 CA265_RS15205 aspartate aminotransferase family protein

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__Pedo557:CA265_RS15205
          Length = 378

 Score =  257 bits (657), Expect = 4e-73
 Identities = 151/376 (40%), Positives = 218/376 (57%), Gaps = 26/376 (6%)

Query: 76  LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQ---ELLDPLRAMLAKT 132
           + D Q ++ ID + G G+ NVGH +P VV A+Q Q A+  +H     E +   +   AK 
Sbjct: 12  IYDAQNKKHIDLIAGIGVSNVGHCHPAVVKAIQEQ-AETYMHLMVYGEYVQTPQVNFAKA 70

Query: 133 LAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATA 192
           LA + P  L  ++F NSGTE+VE A+KLAK Y   +G   FIA   A+HG + GA S   
Sbjct: 71  LADILPESLSCTYFLNSGTEAVEGAMKLAKRYTGRKG---FIACKNAYHGSTQGAESLME 127

Query: 193 KSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPG 252
              +   + P LP    +   N+  +    NE       +AAV +EPIQGE G+ +    
Sbjct: 128 SDFYSSGYGPFLPHVSFIEHNNLADLEKITNE-------IAAVFIEPIQGEAGIRVSDLS 180

Query: 253 YLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGAT 312
           Y+ A+R  C E G L+I DE+Q+G GR+GKMFA EH NV PD+L LAK +GGG MPIGA 
Sbjct: 181 YMQALRTKCTETGTLLIFDEIQSGFGRSGKMFAFEHYNVVPDVLLLAKGIGGG-MPIGAF 239

Query: 313 IATEEVFSVLFDNPFL-HTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFR 371
           I++ E+ SVL   P L H TTFGG+P+ CAA LAT+  L++ ++  + E+KG +    F+
Sbjct: 240 ISSLEIMSVLSHTPILGHMTTFGGHPVCCAAGLATLRTLVDDHIVDEVEEKGQL----FK 295

Query: 372 QLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPL 431
           QL +     ++E RGKG+++A+EF + EI            VL    L+ + ++RI PPL
Sbjct: 296 QLLQH--PAIKEIRGKGLMLAVEFENFEINKKIIDACILDGVLSDWFLHCSNSMRIAPPL 353

Query: 432 TLTIEQ----CELVIK 443
            +T E+    C +++K
Sbjct: 354 IITKEEIAEACTIILK 369


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: 419
Number of extensions: 31
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: 378
Length adjustment: 31
Effective length of query: 428
Effective length of database: 347
Effective search space:   148516
Effective search space used:   148516
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: 50 (23.9 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