GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_0465
          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.

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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