GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Dinoroseobacter shibae DFL-12

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 3609503 Dshi_2887 succinic semialdehyde dehydrogenase (RefSeq)

Query= BRENDA::P51650
         (523 letters)



>FitnessBrowser__Dino:3609503
          Length = 492

 Score =  524 bits (1349), Expect = e-153
 Identities = 265/476 (55%), Positives = 345/476 (72%), Gaps = 5/476 (1%)

Query: 46  LLRGDSFVGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103
           LL   ++  G W      ATFPV +PA G  +  V D G  E   A+ AA  A   W   
Sbjct: 17  LLASKAYFAGAWTDADSGATFPVTNPARGDVIAHVPDLGRAETARAIAAADAAQKPWAAR 76

Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163
           + K+R+ +LR+W+DL++ N D+LA+I+TAE GKPL EA+GE++Y A F+EWF+EEA+R+Y
Sbjct: 77  TAKDRAQVLRRWFDLIVGNADDLARILTAEMGKPLAEARGEVMYGASFVEWFAEEAKRLY 136

Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223
           G+ I     D R  V++QP+GV   ITPWNFP AMITRK   ALAAGC  + KPAEDTP 
Sbjct: 137 GETIPGHLPDARIQVIRQPIGVVGAITPWNFPIAMITRKAAPALAAGCAFLSKPAEDTPL 196

Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283
           SALALA LA +AGIP G++ V+P S + A  +G+  C +  V K++FTGST  G+ILL  
Sbjct: 197 SALALAVLAERAGIPAGLFAVLPSSDSSA--IGKEFCENHTVRKLTFTGSTQVGRILLAQ 254

Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343
           AA+ VK+ SMELGG APFIVFD A++D+AV GAMA KFRNAGQTCVC+NR  VQ G++D+
Sbjct: 255 AADQVKKCSMELGGNAPFIVFDDADLDKAVEGAMACKFRNAGQTCVCANRIYVQDGVYDA 314

Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403
           F  K A A+++ L+VG+G  EG T GPLIN  AVEKV+ H++D  AKG TVVTGG+ H  
Sbjct: 315 FAEKLAAAVEE-LKVGDGAAEGVTIGPLINMPAVEKVQDHLDDLRAKGGTVVTGGETHPL 373

Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463
           GG FF PT+++ VT++M    EETFGPVAP+ +F +E+E +A+AN    GLAGYFY++D 
Sbjct: 374 GGTFFTPTVVTGVTQEMKVAREETFGPVAPLFRFTEEDEVIAMANDTIFGLAGYFYARDI 433

Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVC 519
            +I RV+E LE G+VG+N G+IS+   PFGGVKQSGLGREGS++GIDEYLE+KY+C
Sbjct: 434 GRITRVSEALEYGIVGINTGIISTEGAPFGGVKQSGLGREGSRHGIDEYLEMKYIC 489


Lambda     K      H
   0.318    0.135    0.400 

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: 638
Number of extensions: 23
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: 523
Length of database: 492
Length adjustment: 34
Effective length of query: 489
Effective length of database: 458
Effective search space:   223962
Effective search space used:   223962
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