GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__SB2B:6937359
          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:

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