GapMind for catabolism of small carbon sources

 

Aligments for a candidate for amaB in Dyella japonica UNC79MFTsu3.2

Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate N515DRAFT_0465 N515DRAFT_0465 aldehyde dehydrogenase (NAD+)

Query= uniprot:Q88CC3
         (496 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_0465 N515DRAFT_0465 aldehyde
           dehydrogenase (NAD+)
          Length = 511

 Score =  527 bits (1357), Expect = e-154
 Identities = 291/510 (57%), Positives = 353/510 (69%), Gaps = 22/510 (4%)

Query: 5   LLERLGVAAEA----YTQGDY----------PVHTPIDGSQIASVKLLGKAETIARIDQA 50
           +L+ LG+ AE       QG++          PV+ P  G  I +V     A+    + +A
Sbjct: 5   ILKALGIGAEHSGTYLGQGEWSRTSDAGALQPVN-PATGEVIGTVHASSAADYETIVKRA 63

Query: 51  QSAFEAWRSVPAPRRGELVRLFGEVLREHKADLGELVSIEAGKITQEGLGEVQEMIDICD 110
           Q AF+ WR+ PAPRRGE VRL GE LR+HK  LG LV++E GKI  EG GEVQEMIDI D
Sbjct: 64  QEAFKTWRTTPAPRRGEAVRLCGEALRKHKDALGSLVALEMGKIKPEGDGEVQEMIDIAD 123

Query: 111 FAVGLSRQLYGLTIASERPGHHMRETWHPLGVVGVISAFNFPVAVWAWNTALALVAGNSV 170
           FAVG SR LYG T+ SERPGH M E +HPLG+VG+ISAFNFPVAVWAWN  LA + G+  
Sbjct: 124 FAVGQSRMLYGYTMHSERPGHRMYEQYHPLGLVGIISAFNFPVAVWAWNAFLAAICGDIC 183

Query: 171 VWKPSEKTPLTALACQALFEKALKAFGDAPAGLAQLVIGGREAGEAMVDDPRVPLVSATG 230
           +WKPS KTPL+A+A   +  +ALKA G  P         G +  +  VDD R+PL+S TG
Sbjct: 184 IWKPSPKTPLSAIATMKICNEALKA-GGFPDIFFLFNDAGTDLSQGFVDDKRIPLISFTG 242

Query: 231 STRMGREVGPRVAARFGRSILELGGNNAMILAPSADLDLAVRGILFSAVGTAGQRCTTLR 290
           ST++GR VG RVA R GRS+LELGGNNA+IL  SADL LA+  I+F AVGTAGQRCTT R
Sbjct: 243 STKVGRMVGERVARRMGRSLLELGGNNAIILDASADLKLAIPAIVFGAVGTAGQRCTTTR 302

Query: 291 RLIVHRSIKDEVVARVKAAYGKV--RIGDPR-KDNLVGPLIDKQSFDAMQGALAKARDEG 347
           RL VH SI  EV  ++ AAY +V  +IGDP     L+GPL  + +  A  GA+ KA+  G
Sbjct: 303 RLFVHESIVGEVTDKLVAAYKQVEGKIGDPTLATTLMGPLNSQDAVQAYLGAVEKAKASG 362

Query: 348 GQVFGGERQLADQYPNAYYVSPAIAEMPAQSD-VVRHETFAPILYVLAYDDFEEALRLNN 406
           G+V  G   L+D+  N  +V P I      SD VV+ ETFAPILY++ +   +EA+ L N
Sbjct: 363 GKVLTGGAALSDRKGN--FVLPTIVTGVKNSDEVVQTETFAPILYIMPFKSLDEAIELQN 420

Query: 407 EVPQGLSSCIFTTDIREAERFQSASGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESG 466
           +VPQGLSS IFT D++ AE++ S++GSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESG
Sbjct: 421 DVPQGLSSAIFTRDLKAAEQYLSSAGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESG 480

Query: 467 SDAWKGYMRRQTNTVNYSRELPLAQGIVFD 496
           SDAWK YMRRQTNT NYS  LPLAQGI FD
Sbjct: 481 SDAWKVYMRRQTNTSNYSDSLPLAQGIKFD 510


Lambda     K      H
   0.318    0.135    0.396 

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: 697
Number of extensions: 28
Number of successful extensions: 4
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: 496
Length of database: 511
Length adjustment: 34
Effective length of query: 462
Effective length of database: 477
Effective search space:   220374
Effective search space used:   220374
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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