GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Acidovorax sp. GW101-3H11

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate Ac3H11_4184 Aldehyde dehydrogenase B (EC 1.2.1.22)

Query= BRENDA::P51650
         (523 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4184 Aldehyde
           dehydrogenase B (EC 1.2.1.22)
          Length = 498

 Score =  554 bits (1427), Expect = e-162
 Identities = 271/480 (56%), Positives = 356/480 (74%), Gaps = 3/480 (0%)

Query: 46  LLRGDSFVGGRWLPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISV 105
           LL+ D  + G+W+   + F V DPA+G KL  VA+ G  +A AA+ AA  A+  WK  + 
Sbjct: 16  LLKTDGLINGQWVVGSSRFDVNDPATGLKLADVANLGPADAEAAIAAANAAWGPWKTKTA 75

Query: 106 KERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGD 165
           KERS +LRKW+DL++ N+D+L +I+TAE GKPL EA+GE+ Y A F+EWF+EEA+R+ G+
Sbjct: 76  KERSIILRKWFDLLMANQDDLGRIMTAEQGKPLAEAKGEVAYGASFVEWFAEEAKRINGE 135

Query: 166 IIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSA 225
            +     ++R +VLKQP+GV + ITPWNFP AMITRKV  ALAAGC VV+KPAE TP +A
Sbjct: 136 TLPQFDNNRRLMVLKQPIGVCAAITPWNFPLAMITRKVAPALAAGCPVVIKPAELTPLTA 195

Query: 226 LALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAA 285
           LA A+LA +AGIP GV+N++P     +  +G+VLC   +V  ISFTGST  G+IL+  +A
Sbjct: 196 LAAAELAIRAGIPAGVFNILPADSDNSIAIGKVLCASDVVRHISFTGSTEVGRILMAQSA 255

Query: 286 NSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFV 345
            +VK++S+ELGG APFIVFD A++D AV GA ASK+RNAGQTCVC+NRF VQ G++D FV
Sbjct: 256 PTVKKMSLELGGNAPFIVFDDADIDSAVEGAFASKYRNAGQTCVCTNRFYVQEGVYDEFV 315

Query: 346 TKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS-- 403
            KFA A  K+ +VGNGFE G  QGPLI E A+ KV++HV+DA+AKG  VV GG+R  +  
Sbjct: 316 AKFA-AKVKTAKVGNGFEAGVNQGPLIEEAALTKVQRHVDDALAKGGQVVAGGQRLTALG 374

Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463
            G FFEPT+++N T DMLC  EETFGP APV KF  E+EA+  AN  + GLA YFYS+D 
Sbjct: 375 SGQFFEPTVVANATADMLCAREETFGPFAPVFKFKTEQEAIDAANNTEFGLASYFYSRDV 434

Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523
            +I+RV E LE GMVG N G++++   PFGGVKQSGLGREGS +G+D+Y+E+KY+C G +
Sbjct: 435 GRIFRVTEALEYGMVGANVGILATEHVPFGGVKQSGLGREGSHHGMDDYVEIKYLCLGDI 494


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: 668
Number of extensions: 26
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: 498
Length adjustment: 34
Effective length of query: 489
Effective length of database: 464
Effective search space:   226896
Effective search space used:   226896
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