GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Nocardioides daejeonensis MJ31

Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate WP_110206897.1 DNK54_RS10510 pyridoxal phosphate-dependent aminotransferase

Query= SwissProt::P58350
         (410 letters)



>NCBI__GCF_003194585.1:WP_110206897.1
          Length = 394

 Score =  190 bits (483), Expect = 6e-53
 Identities = 126/370 (34%), Positives = 192/370 (51%), Gaps = 23/370 (6%)

Query: 44  IILGAGEPDFDTPEHVKQAASDAIHRGETKYTALDGTPELKKAIREKFQRENGLAYELD- 102
           I LG G PD D P  V +AA  A+  G  +Y    G  EL++AI     R  GL  + D 
Sbjct: 29  INLGQGFPDADGPASVVEAAVSALRNGRNQYAPGIGVRELREAIARHQHRHYGLDLDPDT 88

Query: 103 EITVATGAKQILFNAMMASLDPGDEVIIPTPYWTSYSDIVHICEG--KPVLIACDASSGF 160
           E+ V TGA + +  A++  +DPGDEV++  PY+ SY  ++    G  +PV +    +  +
Sbjct: 89  EVVVTTGATEGIAAALLGLVDPGDEVVVLEPYYDSYLAMIAFAGGVRRPVTLR---APDY 145

Query: 161 RLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADYRPLLEVLLRHPHVWLLVDDMYEHI 220
           RL    L+AA+T RTR +LLNSP NP+G      + + + ++ + H  V ++ D++YEH+
Sbjct: 146 RLDVAALQAAVTDRTRVILLNSPHNPTGTVLRPEELQAIADLAIEHDLV-VVTDEVYEHL 204

Query: 221 VYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGWRIGYAGGPRELIKAMAVVQSQATS 280
           V+DG R V    L PG+  RT+T++   K+++ TGW++G+A GP +L+ A+   +   + 
Sbjct: 205 VFDGHRHVPLCTL-PGMFERTVTLSSAGKSFSFTGWKVGWATGPADLVGAVLAAKQWLSF 263

Query: 281 CPSSISQAASVAALNGPQDFLKERTESFQRRRDLVVNGLNAIDGLDCRVPEGAFYTFSGC 340
              S  Q A   AL+      +E     Q RRDL+ +GL A+D LD R+PEG ++  +  
Sbjct: 264 TSGSPLQPAIAHALDHEWRAYEELAADLQLRRDLLCSGLAALD-LDVRIPEGTYFALT-- 320

Query: 341 AGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGSAF-----GLSPFFRISYATSEAEL 395
             V     P G+       FC  L E A V  +P   F           R ++    A  
Sbjct: 321 -DVRALGWPDGRA------FCLALPERAGVVAIPTQGFHDDQEAGRHLVRWAFCKDAAVT 373

Query: 396 KEALERIAAA 405
            E LER+A A
Sbjct: 374 TEGLERLARA 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: 380
Number of extensions: 22
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: 410
Length of database: 394
Length adjustment: 31
Effective length of query: 379
Effective length of database: 363
Effective search space:   137577
Effective search space used:   137577
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 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