GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Sphingomonas koreensis DSMZ 15582

Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate Ga0059261_1558 Ga0059261_1558 Aspartate/tyrosine/aromatic aminotransferase

Query= SwissProt::P58350
         (410 letters)



>FitnessBrowser__Korea:Ga0059261_1558
          Length = 389

 Score =  160 bits (404), Expect = 8e-44
 Identities = 121/392 (30%), Positives = 193/392 (49%), Gaps = 23/392 (5%)

Query: 19  SSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKYTALD 78
           S++G +    + +RA AM       I LG G PD +    V +AA+DA+     +Y  + 
Sbjct: 10  SALGTTIFETMSSRARAMG-----AINLGQGFPDGEGCVPVIRAAADALTTRSNQYPPMA 64

Query: 79  GTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPYWTSY 138
           G P L++AI   + R   L    +E+ V +GA + +  +  A + PGDEVI+  P + +Y
Sbjct: 65  GLPALRQAIATHYTRHQQLDLSPEEVIVTSGATEAIAASFTALIAPGDEVILIQPLYDAY 124

Query: 139 SDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADYRP 198
             +V    G   L   +  S +RLT   LEAA  PRTR +++N+P NP+GA  S  +   
Sbjct: 125 LPLVQRAGGVARLARLEPGS-WRLTPAALEAAAGPRTRLIVVNNPVNPAGAKLSHGELAD 183

Query: 199 LLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGWRI 258
           L    +    +  + D+++EH+VYD  R + P    PG+++RT+ +    K +A+TGW++
Sbjct: 184 LAAFCVERDLI-AICDEVWEHVVYDSARHI-PLIAMPGMRDRTVKIGSAGKIFALTGWKV 241

Query: 259 GYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDLVVNG 318
           G+      L   +A      T   +   Q A    L     ++ +    FQR RD +  G
Sbjct: 242 GWMCAAAPLAAVLARAHQFLTFSTAPNLQWAVAEGLETQDAWIADSIVGFQRSRDRLAAG 301

Query: 319 LNAIDGLDCRV-PEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGSA 377
           L A      RV P GA +  S        +  SG  +  D  FC  L+E+  VA +P SA
Sbjct: 302 LTA---AGYRVLPSGATWFLS------IDLAASGIALH-DAAFCDRLVEEIGVAAIPVSA 351

Query: 378 F----GLSPFFRISYATSEAELKEALERIAAA 405
           F     ++   R+ +A ++A L  A+ER++AA
Sbjct: 352 FYAEAPVTHLARLCFAKADAVLDTAIERMSAA 383


Lambda     K      H
   0.318    0.134    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: 374
Number of extensions: 22
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: 410
Length of database: 389
Length adjustment: 31
Effective length of query: 379
Effective length of database: 358
Effective search space:   135682
Effective search space used:   135682
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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