GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Dino:3609503 Dshi_2887 succinic semialdehyde
           dehydrogenase (RefSeq)
          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 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