GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Caulo:CCNA_03242
          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.

Links

Downloads

Related tools

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