GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Neptunomonas antarctica S3-22

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_054341789.1 Nant_RS11485 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P51650
         (523 letters)



>NCBI__GCF_001305295.1:WP_054341789.1
          Length = 493

 Score =  539 bits (1388), Expect = e-157
 Identities = 268/478 (56%), Positives = 353/478 (73%), Gaps = 5/478 (1%)

Query: 46  LLRGDSFVGGRWLPTPA--TFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103
           LL+  +F+ G+W    +   F V +PA+GA L  V+D G  E   A+ AA  A+ +W+  
Sbjct: 17  LLQTQAFIDGQWCEANSGQRFTVSNPANGAPLAEVSDLGTDEVLQAISAAERAWPNWRAH 76

Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163
           + KER ++LR+W++L++  K++LA ++TAE GKPL EA+GE+LY A F+EWF+EEA+R+Y
Sbjct: 77  TGKERGAILRRWFELILAAKEDLAILMTAEQGKPLNEARGEVLYGASFVEWFAEEAKRLY 136

Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223
           GDII    +DKR +VLKQP+GVA+ ITPWNFP AMITRKV  ALAAGC VV+KP+E TP 
Sbjct: 137 GDIIPAHGRDKRLMVLKQPIGVAAAITPWNFPIAMITRKVAPALAAGCPVVIKPSELTPL 196

Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283
           SALALA+LA +AG P GV+NV+  + T A EVG +LC D  V K+SFTGST  GK+L   
Sbjct: 197 SALALAKLAQEAGFPDGVFNVV--TSTNAPEVGRILCADSRVRKLSFTGSTPVGKLLAQQ 254

Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343
            A +VK+VS+ELGG APFIVFD A++D AV GAM SKFRNAGQTCVC+NR  VQ  ++++
Sbjct: 255 CAANVKKVSLELGGNAPFIVFDDADLDAAVVGAMVSKFRNAGQTCVCTNRIFVQENVYEA 314

Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403
           F  KF  A+ ++L+ GNG +EG   GPLI+E+A+ KVE  V DA+  GAT++TGGKR  +
Sbjct: 315 FAEKFRVAV-EALKTGNGADEGVEIGPLIDERALAKVESLVADALENGATLLTGGKRFSA 373

Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463
             N ++PT+LSNV   M    EE FGPVA +I F  E E +A+AN    GLA YFY++D 
Sbjct: 374 VSNGYQPTVLSNVNNQMRIAQEEIFGPVATLIPFQSESEVIAMANDTPSGLAAYFYARDI 433

Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYG 521
            ++WRV+E LE GMVGVNEG+IS+   PFGG+K+SGLGREGSKYGID+Y+E+KY+C G
Sbjct: 434 GRVWRVSEALEYGMVGVNEGIISTEVAPFGGIKESGLGREGSKYGIDDYVELKYICLG 491


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: 641
Number of extensions: 20
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: 493
Length adjustment: 34
Effective length of query: 489
Effective length of database: 459
Effective search space:   224451
Effective search space used:   224451
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 24 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