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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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