Alignments for a candidate for adh in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Stenotrophomonas chelatiphaga DSM 21508

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate WP_057506719.1 ABB28_RS00370 aldehyde dehydrogenase family protein

Query= BRENDA::P49419
         (539 letters)



>NCBI__GCF_001431535.1:WP_057506719.1
          Length = 510

 Score =  532 bits (1371), Expect = e-155
 Identities = 283/503 (56%), Positives = 339/503 (67%), Gaps = 6/503 (1%)

Query: 42  LKELGLREENEGVY--NGSWGGR--GEVITTYCPANNEPIARVRQASVADYEETVKKARE 97
           LK LGL   N G Y  NG W     GE+IT   P   E IA+VR  +  +YE  + +A+E
Sbjct: 6   LKALGLDAINAGTYLGNGEWSTATGGELITPVNPTTGEAIAQVRATTADEYETVIARAQE 65

Query: 98  AWKIWADIPAPKRGEIVRQIGDALREKIQVLGSLVSLEMGKILVEGVGEVQEYVDICDYA 157
           A+KIW   PAP+RGE VR  G+ALR     LGSLV+LEMGK   EG GEVQE +DI D+A
Sbjct: 66  AFKIWRTTPAPRRGEAVRLCGEALRANKDALGSLVALEMGKSKPEGDGEVQEMIDIADFA 125

Query: 158 VGLSRMIGGPILPSERSGHALIEQWNPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLW 217
           VG SRM+ G  + SER GH + EQ+ P+GLVGII+AFNFPVAV+ WN  +A +CG++CLW
Sbjct: 126 VGQSRMLYGYTMHSERPGHRMYEQYQPLGLVGIISAFNFPVAVWAWNAFLATVCGDICLW 185

Query: 218 KGAPTTSLISVAVTKIIAKVLEDNKLPGAICSLTCGGADIGTAMAKDERVNLLSFTGSTQ 277
           K +  T L ++A  +I  + L D   P     +   G  +   M  D+RV L+SFTGSTQ
Sbjct: 186 KPSNKTPLTAIASMRICNEALRDAGFPDLFFLINDAGTALSETMVADKRVPLISFTGSTQ 245

Query: 278 VGKQVGLMVQERFGRSLLELGGNNAIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLF 337
           VG+ V   V  R GR LLELGGNNAII  E ADL L +P  +F AVGTAGQRCTT RRL 
Sbjct: 246 VGRTVAEKVAHRLGRCLLELGGNNAIILDETADLKLAIPGIVFGAVGTAGQRCTTTRRLI 305

Query: 338 IHESIHDEVVNRLKKAYAQI--RVGNPWDPNVLYGPLHTKQAVSMFLGAVEEAKKEGGTV 395
           +HESIHD+V+  L KAY Q+  ++G+P DP  L GPL++  AV  FL ++E+AK  GGTV
Sbjct: 306 VHESIHDDVLATLVKAYKQVEGKIGDPTDPANLMGPLNSDGAVQQFLASIEKAKASGGTV 365

Query: 396 VYGGKVMDRPGNYVEPTIVTGLGHDASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGL 455
             GG  +DR GN+V P IVTGL +   +   ETFAPILYV K+   +E     N V QGL
Sbjct: 366 QTGGTRIDRAGNFVLPAIVTGLKNSDEVVQHETFAPILYVMKYSTLDEAIDMQNGVPQGL 425

Query: 456 SSSIFTKDLGRIFRWLGPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQ 515
           SSSIFT +L    R+L   GSDCGI NVNI TSGAEIGGAFGGEK TGGGRESGSDAWK 
Sbjct: 426 SSSIFTTNLKTAERFLSAAGSDCGIANVNIGTSGAEIGGAFGGEKDTGGGRESGSDAWKV 485

Query: 516 YMRRSTCTINYSKDLPLAQGIKF 538
           YMRR T TINYS  LPLAQGIKF
Sbjct: 486 YMRRQTNTINYSDSLPLAQGIKF 508


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: 828
Number of extensions: 33
Number of successful extensions: 2
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: 510
Length adjustment: 35
Effective length of query: 504
Effective length of database: 475
Effective search space:   239400
Effective search space used:   239400
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 24 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
the source code
instructions for running GapMind on your computer

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