GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dopDH in Shewanella amazonensis SB2B

Align α-ketoglutaric semialdehyde dehydrogenase subunit (EC 1.2.1.26) (characterized)
to candidate 6937359 Sama_1529 fatty aldehyde dehydrogenase (RefSeq)

Query= metacyc::G1G01-1343-MONOMER
         (525 letters)



>lcl|FitnessBrowser__SB2B:6937359 Sama_1529 fatty aldehyde
           dehydrogenase (RefSeq)
          Length = 515

 Score =  417 bits (1072), Expect = e-121
 Identities = 222/492 (45%), Positives = 308/492 (62%), Gaps = 3/492 (0%)

Query: 17  SRDAIRAIDPTTGQTLEPAYLGGTGEHVAQACALAWAAFDAYRETSLEQRAEFLEAIATQ 76
           S  +    +P+T   L  A+  GT   V  A   A AAF  +++TS +Q+A+ LE +A +
Sbjct: 18  SEASFTRFNPSTNSVLPGAFSQGTVVEVEAAAIAADAAFWEFQQTSADQKAKLLETMAKE 77

Query: 77  IEALGDALIDRAVIETGLPKARIQGERGRTCTQLRTFARTVRAGEWLDVRIDSALPERQP 136
           IE  GDA++  A++E+GLP+AR++GE GRT  QLR FA  +R   +  + +D A P+RQP
Sbjct: 78  IEQDGDAIVACAMLESGLPEARLKGELGRTAGQLRLFASVLRE-PYSPLLMDKANPDRQP 136

Query: 137 LPRADLRQRQVALGPVAVFGASNFPLAFSVAGGDTASALAAGCPVVVKAHSAHPGTSELV 196
           LP+ +L+  Q+ LG VAVFGASNFPLAFS AGGDTASALAAGC V+VK H +HPGTSELV
Sbjct: 137 LPKPELKLGQLPLGVVAVFGASNFPLAFSTAGGDTASALAAGCAVIVKGHPSHPGTSELV 196

Query: 197 GQAVAQAVKQCGLPEGVFSLLYGSGREVGIALVSDPRIKAVGFTGSRSGGMALCQAAQAR 256
            +A+A+A+   G+P+G+FSL+ GS   + +ALV  P +KAVGFTGS   G  L      R
Sbjct: 197 ARAMARAIDLTGMPKGLFSLIQGSEPALSVALVEHPLVKAVGFTGSLKVGRLLADRCALR 256

Query: 257 PEPIPVYAEMSSINPVFLFDAALQARAEALAQGFVASLTQGAGQFCTNPGLVIARQGPAL 316
           PEPIP Y E+ S+NP  L    L   A  LA+  V S+  G GQFCT+PGLVIA +GP L
Sbjct: 257 PEPIPFYGELGSVNPQLLLPGKLARDAAVLAEAQVNSMMMGHGQFCTSPGLVIAIKGPGL 316

Query: 317 QRFITAAAGYVQQGAAQTMLTPGIFSAYQAGIAALADNPHAQAITSGQAGQGPNQCQAQL 376
           + ++ A +    +  A  ML+ GI  A+   ++ L   P    I  GQA +  +  +  +
Sbjct: 317 ESYLAALSDIASRQNAAAMLSAGICQAFNQDVSILV--PRVNVIAQGQAAEAAHHSRPLI 374

Query: 377 FVTQAEAFLADPALQAEVFGAASLVVACTDDEQVRQVAEHLEGQLTATLQLDEADIDSAR 436
              +A A    P L  E+FG  +LV  C   E++ ++ + L GQLT ++   E ++    
Sbjct: 375 ASIEASALFGQPELLEEIFGPFALVAICDSKEEMFELVKRLPGQLTGSIHGLETEVADFG 434

Query: 437 ALLPTLERKAGRILVNGWPTGVEVCDAMVHGGPFPATSDARTTSVGTAAILRFLRPVCYQ 496
            ++  L  K GRI+ N  PTGVEV  AM HGGP+PA++D R+TSVG  A+ RF+RP+CYQ
Sbjct: 435 DIIDRLAFKVGRIMFNQMPTGVEVARAMNHGGPYPASTDGRSTSVGAEAMKRFMRPICYQ 494

Query: 497 DVPDALLPQALK 508
           ++P+ LLP  LK
Sbjct: 495 NMPETLLPNELK 506


Lambda     K      H
   0.319    0.134    0.391 

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: 680
Number of extensions: 21
Number of successful extensions: 3
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: 525
Length of database: 515
Length adjustment: 35
Effective length of query: 490
Effective length of database: 480
Effective search space:   235200
Effective search space used:   235200
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 (21.8 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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