GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS32650
          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 (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