GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4184
          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 (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