GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Dyadobacter tibetensis Y620-1

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_025763135.1 X939_RS0110060 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= BRENDA::P42588
         (459 letters)



>NCBI__GCF_000566685.1:WP_025763135.1
          Length = 384

 Score =  190 bits (483), Expect = 6e-53
 Identities = 132/384 (34%), Positives = 204/384 (53%), Gaps = 31/384 (8%)

Query: 76  LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAA 135
           L D  G E++D  GG  + +VGH +P  V+ +  QL+K   +S  +  P +  LA  L  
Sbjct: 23  LWDQNGIEYLDMYGGHAVISVGHCHPDYVARLTEQLSKISFYSNSVQIPQQEELATKLGT 82

Query: 136 LTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAKST 195
           L+       F CNSG E+ E ALKLA  +    G+   +A + AFHG++ GA++AT   +
Sbjct: 83  LSGYPDYKLFLCNSGAEANENALKLASFHT---GRKKVVAFTKAFHGRTAGAVAATDNPS 139

Query: 196 FRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYLT 255
              P +        +PF +IEA++  + E      +VAAVI+E IQG GG+ +    +L 
Sbjct: 140 IVAP-VNYNEHVSFLPFNDIEALQAGITE------EVAAVIVEGIQGVGGIQVCSDEFLQ 192

Query: 256 AVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIAT 315
           A+RK CDE GA +ILD VQ G GRTGK F+ +   + PD++ +AK +G G    G  IA 
Sbjct: 193 ALRKRCDETGAALILDSVQCGYGRTGKFFSHQFSGIHPDMMTMAKGMGNGFPIAGVLIAP 252

Query: 316 EEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLAR 375
           +  F   F    L  TTFGGN LACAA +A ++++ ++ L   A + G  L     +L  
Sbjct: 253 Q--FKASFG---LLGTTFGGNHLACAAGIAVLDIMKDEQLLDNATKIGAYLFHEIEELG- 306

Query: 376 EYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVL----VAGTLNNAKTIRIEPPL 431
            Y DL    RG+G+++ IEF       +F  +  R ++L    +   +  A T+R+ P L
Sbjct: 307 GYKDL----RGRGLMIGIEF-------DFPVKELRNKLLFEHHIFTGVAGAYTLRLLPSL 355

Query: 432 TLTIEQCELVIKAARKALAAMRVS 455
            ++ ++ +  ++A R  L   + S
Sbjct: 356 AISQKEADQFLEAYRSCLKTFQQS 379


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: 381
Number of extensions: 15
Number of successful extensions: 6
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: 384
Length adjustment: 32
Effective length of query: 427
Effective length of database: 352
Effective search space:   150304
Effective search space used:   150304
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 24 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