GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Burkholderia phytofirmans PsJN

Align Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized)
to candidate BPHYT_RS32650 BPHYT_RS32650 aldehyde dehydrogenase

Query= SwissProt::Q64057
         (539 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS32650 BPHYT_RS32650 aldehyde
           dehydrogenase
          Length = 499

 Score =  481 bits (1237), Expect = e-140
 Identities = 241/478 (50%), Positives = 330/478 (69%), Gaps = 7/478 (1%)

Query: 66  ITTYCPANNEPIARVRQASMKDYEETIGKAKKAWNIWADIPAPKRGEIVRKIGDALREKI 125
           I  + P   + I RV   ++ + +  + +AK+A+  W ++PAP+RGE+VR +G+ LREK 
Sbjct: 21  IAVHSPITGDLIGRVASNTVAEVDTALARAKEAYTAWRNVPAPRRGELVRLLGNRLREKK 80

Query: 126 QLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGGPTLPSERPGHALMEQWNPL 185
           Q LG +++LE GKIL EG+GEVQE +D+CD+A GLSR + G T+ SERPGH + E W+P+
Sbjct: 81  QALGSIITLETGKILQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHRMAETWHPM 140

Query: 186 GLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSIAVTKIIAKVLED-NLLP 244
           G   +I+AFNFP AV+ WN A+AL+ GN  +WK +  T L ++AV +I+ + L++    P
Sbjct: 141 GTCVVISAFNFPAAVWSWNAALALVCGNAVIWKPSEKTPLTALAVNQILTEALQEFGDAP 200

Query: 245 GAICSLTCGGADMGTAMARDERVNLLSFTGSTQVGKQVALMVQERFGKSLLELGGNNAII 304
             + +L  GG D+G  +  D R +++S TGST++G+ V + V +RFG+SLLELGGNNA I
Sbjct: 201 AGLTALINGGRDVGAKLVADPRASIVSATGSTEMGRTVGVEVAKRFGRSLLELGGNNAGI 260

Query: 305 AFEDADLSLVLPSALFAAVGTAGQRCTTVRRLFLHESIHDEVVDRLKNAYSQIRVGNPWD 364
             + AD  L +   LF+AVGTAGQRCT++RRLF+HES++D+ ++RLK  YS++ +GNP +
Sbjct: 261 VTQTADHELAMRGILFSAVGTAGQRCTSLRRLFVHESVYDKTIERLKQLYSKVPIGNPLE 320

Query: 365 PNILYGPLHTKQAVSMFVQAVEEAKKEGGTVVYGGKVMD----HPGNYVEPTIVTGLVHD 420
              L GPL  KQ+     +A+++A  EGG  V+GG+ +D      G YV P IV  +   
Sbjct: 321 KGTLMGPLIDKQSYGRMQEALQQATAEGGK-VFGGERVDVKGYENGYYVRPAIVE-MPSQ 378

Query: 421 APIVHKETFAPILYVFKFKNEEEVFEWNNEVKQGLSSSIFTKDLGRIFRWLGPKGSDCGI 480
             +V KETFAPILYV ++ +  +  E NN    GLSS +FT DL    R+L   GSDCGI
Sbjct: 379 TSVVLKETFAPILYVLRYTDFADAVEANNAAVHGLSSCVFTTDLREAERFLSDSGSDCGI 438

Query: 481 VNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYMRRSTCTINYSTALPLAQGIKF 538
            NVNI  SGAEIGGAFGGEK TGGGRESGSDAWK YMRR+T T+NYS+ALPLAQGI F
Sbjct: 439 ANVNIGPSGAEIGGAFGGEKETGGGRESGSDAWKAYMRRATNTVNYSSALPLAQGIDF 496


Lambda     K      H
   0.319    0.137    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: 803
Number of extensions: 31
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 ( 7.4 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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