Alignments for a candidate for adh in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Dyella japonica UNC79MFTsu3.2

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate N515DRAFT_0465 N515DRAFT_0465 aldehyde dehydrogenase (NAD+)

Query= BRENDA::P49419
         (539 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0465
          Length = 511

 Score =  529 bits (1363), Expect = e-155
 Identities = 278/504 (55%), Positives = 344/504 (68%), Gaps = 7/504 (1%)

Query: 42  LKELGLREENEGVY--NGSWGGRGEV--ITTYCPANNEPIARVRQASVADYEETVKKARE 97
           LK LG+  E+ G Y   G W    +   +    PA  E I  V  +S ADYE  VK+A+E
Sbjct: 6   LKALGIGAEHSGTYLGQGEWSRTSDAGALQPVNPATGEVIGTVHASSAADYETIVKRAQE 65

Query: 98  AWKIWADIPAPKRGEIVRQIGDALREKIQVLGSLVSLEMGKILVEGVGEVQEYVDICDYA 157
           A+K W   PAP+RGE VR  G+ALR+    LGSLV+LEMGKI  EG GEVQE +DI D+A
Sbjct: 66  AFKTWRTTPAPRRGEAVRLCGEALRKHKDALGSLVALEMGKIKPEGDGEVQEMIDIADFA 125

Query: 158 VGLSRMIGGPILPSERSGHALIEQWNPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLW 217
           VG SRM+ G  + SER GH + EQ++P+GLVGII+AFNFPVAV+ WN  +A ICG++C+W
Sbjct: 126 VGQSRMLYGYTMHSERPGHRMYEQYHPLGLVGIISAFNFPVAVWAWNAFLAAICGDICIW 185

Query: 218 KGAPTTSLISVAVTKIIAKVLEDNKLPGAICSLTCGGADIGTAMAKDERVNLLSFTGSTQ 277
           K +P T L ++A  KI  + L+    P         G D+      D+R+ L+SFTGST+
Sbjct: 186 KPSPKTPLSAIATMKICNEALKAGGFPDIFFLFNDAGTDLSQGFVDDKRIPLISFTGSTK 245

Query: 278 VGKQVGLMVQERFGRSLLELGGNNAIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLF 337
           VG+ VG  V  R GRSLLELGGNNAII    ADL L +P+ +F AVGTAGQRCTT RRLF
Sbjct: 246 VGRMVGERVARRMGRSLLELGGNNAIILDASADLKLAIPAIVFGAVGTAGQRCTTTRRLF 305

Query: 338 IHESIHDEVVNRLKKAYAQI--RVGNPWDPNVLYGPLHTKQAVSMFLGAVEEAKKEGGTV 395
           +HESI  EV ++L  AY Q+  ++G+P     L GPL+++ AV  +LGAVE+AK  GG V
Sbjct: 306 VHESIVGEVTDKLVAAYKQVEGKIGDPTLATTLMGPLNSQDAVQAYLGAVEKAKASGGKV 365

Query: 396 VYGGKVM-DRPGNYVEPTIVTGLGHDASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQG 454
           + GG  + DR GN+V PTIVTG+ +   +  TETFAPILY+  FK+ +E     N+V QG
Sbjct: 366 LTGGAALSDRKGNFVLPTIVTGVKNSDEVVQTETFAPILYIMPFKSLDEAIELQNDVPQG 425

Query: 455 LSSSIFTKDLGRIFRWLGPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWK 514
           LSS+IFT+DL    ++L   GSDCGI NVNI TSGAEIGGAFGGEK TGGGRESGSDAWK
Sbjct: 426 LSSAIFTRDLKAAEQYLSSAGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWK 485

Query: 515 QYMRRSTCTINYSKDLPLAQGIKF 538
            YMRR T T NYS  LPLAQGIKF
Sbjct: 486 VYMRRQTNTSNYSDSLPLAQGIKF 509


Lambda     K      H
   0.318    0.136    0.417 

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: 846
Number of extensions: 34
Number of successful extensions: 3
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: 539
Length of database: 511
Length adjustment: 35
Effective length of query: 504
Effective length of database: 476
Effective search space:   239904
Effective search space used:   239904
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources