GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Caulobacter crescentus NA1000

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate CCNA_03242 CCNA_03242 succinic semialdehyde dehydrogenase

Query= BRENDA::P51650
         (523 letters)



>lcl|FitnessBrowser__Caulo:CCNA_03242 CCNA_03242 succinic
           semialdehyde dehydrogenase
          Length = 485

 Score =  535 bits (1378), Expect = e-156
 Identities = 264/479 (55%), Positives = 349/479 (72%), Gaps = 3/479 (0%)

Query: 45  DLLRGDSFVGGRWLPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEIS 104
           +L+   + + G+W+   A+F V +PA G  +  VAD G  E   A+ AA+ A  +W   +
Sbjct: 8   NLVETAALIDGQWVRGEASFDVLNPADGTLIAAVADLGAAETTLAIDAAHRALPAWAART 67

Query: 105 VKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYG 164
            KER ++LR+W DL++ + D+LA+++T E GKPL EA+GE++Y A F++WF+EEA+R YG
Sbjct: 68  AKERGAILRRWSDLILAHADDLARLMTDEQGKPLAEAKGEVVYGASFIDWFAEEAKRAYG 127

Query: 165 DIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYS 224
             I T    KR   +KQPVGV + I PWNFP AMITRKVG ALAAGCTVVVKPA +TP S
Sbjct: 128 HTIPTPMPGKRLASIKQPVGVCAAIAPWNFPIAMITRKVGPALAAGCTVVVKPAAETPLS 187

Query: 225 ALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHA 284
           ALA+A+LA +AG+P GV N++  + T++ EVG+VLC D  V K+SFTGST  GK+L    
Sbjct: 188 ALAIARLATEAGVPAGVLNIV--TTTRSSEVGKVLCDDSRVRKLSFTGSTPIGKVLYQQC 245

Query: 285 ANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSF 344
           A ++K++S+ELGG APFIVFD A+++ AV GA+ASK+RNAGQTCVC+NR +VQ GIHD+F
Sbjct: 246 AGTMKKLSLELGGNAPFIVFDDADLEAAVDGAIASKYRNAGQTCVCANRLIVQSGIHDAF 305

Query: 345 VTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQSG 404
             + AE +  +L+VG G  EG   GPLINEKA+ KV   V+ AV  GA V+TGG  H  G
Sbjct: 306 AARLAEKV-AALKVGPGTGEGVQIGPLINEKALTKVVGLVSGAVQAGAEVLTGGDVHGLG 364

Query: 405 GNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDPA 464
           G+F++PT+L   T +M    EE FGPVAP++KF+ E EAV +ANA   GLA YFYS+D  
Sbjct: 365 GHFYQPTVLVGATPEMRIFQEEIFGPVAPIVKFETEAEAVELANATPFGLAAYFYSRDVG 424

Query: 465 QIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523
           + WRVAEQ+E GMVG+NEGLIS+   PFGGVK+SGLGREG+  G+DEYLE KY+C+GG+
Sbjct: 425 RCWRVAEQIEAGMVGINEGLISTEVAPFGGVKESGLGREGASEGLDEYLETKYLCFGGV 483


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: 678
Number of extensions: 27
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: 485
Length adjustment: 34
Effective length of query: 489
Effective length of database: 451
Effective search space:   220539
Effective search space used:   220539
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