Alignments for a candidate for adh in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Paraburkholderia bryophila 376MFSha3.1

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate H281DRAFT_01833 H281DRAFT_01833 aldehyde dehydrogenase (NAD+)

Query= BRENDA::P49419
         (539 letters)



>FitnessBrowser__Burk376:H281DRAFT_01833
          Length = 499

 Score =  479 bits (1234), Expect = e-140
 Identities = 243/478 (50%), Positives = 327/478 (68%), Gaps = 7/478 (1%)

Query: 66  ITTYCPANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEIVRQIGDALREKI 125
           I  + P N E I RV   +VA+ +  +  A++A+  W ++PAP+RGE+VR +G+ LRE+ 
Sbjct: 21  IAVHSPINGELIGRVASRTVAEVDAALASAQKAYASWRNVPAPRRGELVRLLGNKLREQK 80

Query: 126 QVLGSLVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPILPSERSGHALIEQWNPV 185
             LGS+++LE GKIL EG+GEVQE +DICD+AVGLSR + G  + SER GH + E W+P+
Sbjct: 81  HALGSIITLETGKILQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHRMAETWHPL 140

Query: 186 GLVGIITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKIIAKVLED-NKLP 244
           G+  +I+AFNFP AV+ WN A+A++CGN  +WK +  T L ++AV KI+   L++    P
Sbjct: 141 GVCTVISAFNFPAAVWSWNAALALVCGNAVVWKPSEKTPLTALAVDKILQDALKEFGDAP 200

Query: 245 GAICSLTCGGADIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGRSLLELGGNNAII 304
             + S+  GG ++G  +  D R N++S TGST++G+ VG+ V  RFGRS+LELGGNNA I
Sbjct: 201 EGLTSVVNGGREVGAKLVADPRSNIVSATGSTEMGRAVGVEVARRFGRSILELGGNNAGI 260

Query: 305 AFEDADLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKKAYAQIRVGNPWD 364
               AD+ L +   +F+AVGTAGQRCT+ RRLF+HES++D+ V RLK  Y+++ +GNP +
Sbjct: 261 VSGSADMELALRGIVFSAVGTAGQRCTSLRRLFVHESVYDKAVERLKALYSKVVIGNPLE 320

Query: 365 PNVLYGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMDRPGN----YVEPTIVTGLGHD 420
             VL GPL  +Q+ +    A+E+AK EGG  V+GG+     GN    YV P IV  +   
Sbjct: 321 QGVLMGPLIDEQSFNRMQAALEQAKSEGGK-VFGGERHAVAGNEKGFYVRPAIVE-MPSQ 378

Query: 421 ASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLGPKGSDCGI 480
            S+   ETFAPILYV K+ + ++    NN    GLSS +FT DL    R+L   GSDCGI
Sbjct: 379 TSVVLKETFAPILYVLKYSDFDDAIGGNNAAVHGLSSCVFTTDLREAERFLSASGSDCGI 438

Query: 481 VNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYMRRSTCTINYSKDLPLAQGIKF 538
            NVNI  SGAEIGGAFGGEK TGGGRESGSD+WK YMRR+T T+NYS  LPLAQGI F
Sbjct: 439 ANVNIGPSGAEIGGAFGGEKETGGGRESGSDSWKAYMRRATNTVNYSSALPLAQGIDF 496


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: 852
Number of extensions: 43
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: 539
Length of database: 499
Length adjustment: 35
Effective length of query: 504
Effective length of database: 464
Effective search space:   233856
Effective search space used:   233856
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