GapMind for catabolism of small carbon sources

 

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

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_067912398.1 AQZ52_RS14300 aldehyde dehydrogenase family protein

Query= metacyc::MONOMER-16244
         (495 letters)



>NCBI__GCF_001519075.1:WP_067912398.1
          Length = 500

 Score =  325 bits (834), Expect = 2e-93
 Identities = 193/476 (40%), Positives = 270/476 (56%), Gaps = 17/476 (3%)

Query: 24  FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83
           FI+ +F+   S + F   +P     + +V  + + DI+ A++AA  A   +W T+    R
Sbjct: 16  FISGKFLPPASGRYFANPTPVDGTVLCEVARSDAADIELALDAAHRAA-PNWGTTSAAER 74

Query: 84  MKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKIKGSVI 142
             +L ++AD ++E+   LA  E+ DNGK L  S   D+ L   +FR  AG     +G + 
Sbjct: 75  AGILNRIADRMEENLALLAQAESWDNGKPLRESMAADLPLAIDHFRYFAGCIRAQQGGLS 134

Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202
           E       Y   EP+GV GQIIPWNFPLLMA+WK+ P L  G   VLK AE TP S +  
Sbjct: 135 EIDSQTVAYHFHEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCIVLKPAEQTPASIMIW 194

Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262
           A L+ +   P GV+N+V+GFG  AG P++S P+I K+AFTG T+TGR IM+ A+E N+  
Sbjct: 195 AELVGDL-LPAGVINIVNGFGLEAGKPLASSPRISKIAFTGETSTGRLIMQYASE-NIIP 252

Query: 263 VTLELGGKSPNIVF------DDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKI 316
           VTLELGGKSPNI F      DD  +   I+  V     N GEVC   SR  + E IYD+ 
Sbjct: 253 VTLELGGKSPNIFFADVAQEDDEFLDKAIEGFVM-FALNQGEVCTCPSRALIHESIYDRF 311

Query: 317 VSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFG--- 373
           +         +K G P   +T +GAQ S  Q++KIL Y+D+G+ EGA  + GG R     
Sbjct: 312 MERALARVAQIKQGHPLDMETMIGAQASTEQVEKILSYLDLGEMEGALTLIGGGRASVPP 371

Query: 374 --NKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHT 431
               G +I+PT+        ++ ++EIFGPVV +T FK   E +++AND+ YGL AGV +
Sbjct: 372 ALKGGNYIQPTVLKG-HNGMRVFQEEIFGPVVCVTTFKDEAEALSIANDTLYGLGAGVWS 430

Query: 432 TNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVK 487
            ++ST   +   I +G +W N Y+ +     FGGY QSGIGRE     L +Y Q K
Sbjct: 431 RDISTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHLMMLSHYQQTK 486


Lambda     K      H
   0.316    0.133    0.389 

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: 570
Number of extensions: 24
Number of successful extensions: 7
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: 495
Length of database: 500
Length adjustment: 34
Effective length of query: 461
Effective length of database: 466
Effective search space:   214826
Effective search space used:   214826
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 (21.6 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