GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Novosphingobium fuchskuhlense FNE08-7

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_067912398.1 AQZ52_RS14300 aldehyde dehydrogenase family protein

Query= BRENDA::A0A0E3T552
         (503 letters)



>NCBI__GCF_001519075.1:WP_067912398.1
          Length = 500

 Score =  322 bits (825), Expect = 2e-92
 Identities = 199/498 (39%), Positives = 279/498 (56%), Gaps = 24/498 (4%)

Query: 11  FIDGEWREPVLKKRIPIINPATEEIIGHIPAATAEDVELAVEAARRALSRNKGRDWASAP 70
           FI G++  P   +      P    ++  +  + A D+ELA++AA RA       +W +  
Sbjct: 16  FISGKFLPPASGRYFANPTPVDGTVLCEVARSDAADIELALDAAHRAAP-----NWGTTS 70

Query: 71  GAVRAKYLRAIAAKIGERKPEIAKLEAIDCGKPLDEA-AWDIDDVSGCFEYYAELAEGLD 129
            A RA  L  IA ++ E    +A+ E+ D GKPL E+ A D+      F Y+A    G  
Sbjct: 71  AAERAGILNRIADRMEENLALLAQAESWDNGKPLRESMAADLPLAIDHFRYFA----GCI 126

Query: 130 AQQKAPISLPMEQFKSHVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCAAILKPSEL 189
             Q+  +S    Q  ++   EP+GVVG I PWN+PLLMA WK+APALAAG   +LKP+E 
Sbjct: 127 RAQQGGLSEIDSQTVAYHFHEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCIVLKPAEQ 186

Query: 190 ASVTCLELADVCREVGLPPGVLNILTGLGHEAGAPLVSHPHVDKIAFTGSTMTGSKIMTA 249
              + +  A++  ++ LP GV+NI+ G G EAG PL S P + KIAFTG T TG  IM  
Sbjct: 187 TPASIMIWAELVGDL-LPAGVINIVNGFGLEAGKPLASSPRISKIAFTGETSTGRLIMQY 245

Query: 250 AAQLVKPVSLELGGKSPIVVF------DDVDIDKAAEWTAFGCFWTN-GQICSATSRLIL 302
           A++ + PV+LELGGKSP + F      DD  +DKA E   F  F  N G++C+  SR ++
Sbjct: 246 ASENIIPVTLELGGKSPNIFFADVAQEDDEFLDKAIE--GFVMFALNQGEVCTCPSRALI 303

Query: 303 HENIATEFLDRLLKWCKNIKIADPLEEGCRLGPVVSGGQYEKILKSIETAKSEGARVLSG 362
           HE+I   F++R L     IK   PL+    +G   S  Q EKIL  ++  + EGA  L G
Sbjct: 304 HESIYDRFMERALARVAQIKQGHPLDMETMIGAQASTEQVEKILSYLDLGEMEGALTLIG 363

Query: 363 GDR---PEHLKKGFFIEPTIITDVTTSMQIWREEVFGPVLCVKTFSSEDEALELANDTHY 419
           G R   P  LK G +I+PT++      M++++EE+FGPV+CV TF  E EAL +ANDT Y
Sbjct: 364 GGRASVPPALKGGNYIQPTVLKG-HNGMRVFQEEIFGPVVCVTTFKDEAEALSIANDTLY 422

Query: 420 GLGAAVISKDLERCDRFSKGLQAGIVWINCSQPCFCQAPWGGNKRSGFGRELGKWGLDNY 479
           GLGA V S+D+  C R  +G++AG VW NC       A +GG K+SG GRE     L +Y
Sbjct: 423 GLGAGVWSRDISTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHLMMLSHY 482

Query: 480 LTVKQVTEYVSDDPWGWY 497
              K +    +    G++
Sbjct: 483 QQTKNLLVSYAPQKLGFF 500


Lambda     K      H
   0.319    0.136    0.424 

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: 644
Number of extensions: 26
Number of successful extensions: 5
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: 503
Length of database: 500
Length adjustment: 34
Effective length of query: 469
Effective length of database: 466
Effective search space:   218554
Effective search space used:   218554
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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