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.

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:

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