GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Sphingomonas koreensis DSMZ 15582

Align Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized)
to candidate Ga0059261_1006 Ga0059261_1006 NAD-dependent aldehyde dehydrogenases

Query= SwissProt::Q8GAK7
         (458 letters)



>FitnessBrowser__Korea:Ga0059261_1006
          Length = 453

 Score =  374 bits (959), Expect = e-108
 Identities = 208/452 (46%), Positives = 270/452 (59%), Gaps = 7/452 (1%)

Query: 5   TIDPTTGITLKTFDAHTPEEVENRIARAEAAFRSLQNTSFEERARWMHKAADILESEADE 64
           +I+P TG    TF A   + +E  + RAEAAFRS + +   +R   +   AD  E+    
Sbjct: 4   SINPATGEAGATFAALDDDAIEAALTRAEAAFRSWRASDIAQRTALLTAIADRFEANKRH 63

Query: 65  VARLIATEMGKTLTTAKYEALKSATGMRHFADHAQRYLSP-ETPVPASEVNASNLHVQFD 123
           +A     EMGKTL +A  E  K   G RH+AD    YL+P ET   +       L     
Sbjct: 64  LAETATKEMGKTLASAIAEVEKCIAGFRHYADKGPGYLAPIETKTASGRAVGHWL----- 118

Query: 124 PLGVVLAVMPWNYPLWQAVRFAAPALMAGNTGLLKHASNVPQCALYLGDLFARGGFPEGA 183
           PLG +LAVMPWN+P WQ VR+ AP ++AGN GLLKHAS    CA  +  + +  G P+G 
Sbjct: 119 PLGPILAVMPWNFPYWQVVRWLAPTILAGNVGLLKHASLTQGCAALIQQMVSAAGAPDGL 178

Query: 184 FQTLLVEGKDVIPLVDDARIRAVTLTGSVAAGSAIAEAAGRNIKRSVLELGGMDVFIVMP 243
           FQ L ++   V  ++ D R+ AVTLTGS  AG+ +AEAAGR +K+ VLELGG D FIVMP
Sbjct: 179 FQNLPIKSDKVSRIIADTRVAAVTLTGSEGAGAKVAEAAGRALKKVVLELGGSDPFIVMP 238

Query: 244 SADIEKAAAQAVIARLQNSGQSCIAAKRFYVHEDVYDRFEHLFVTGMAEAVAGDPLDEST 303
           SAD++KA A AV AR+QN+GQSCI AKR  VH DVYD F   F   M     GDP+++  
Sbjct: 239 SADLDKAVATAVKARVQNAGQSCICAKRMIVHADVYDAFLDKFTAAMLAVKIGDPMEDGV 298

Query: 304 SFGPLATERGRQDVHELVRDAREKGAAVQCGGEIPEGEGWYYPATVLTGVTEDMRIYREE 363
             GPL++   R  V E V  A   GA +  G +I E +G +  A VLT V  D    +EE
Sbjct: 299 EMGPLSSVEQRDTVLEQVERAVADGATLAGGAKI-ERDGAWMEAGVLTHVHPDADFAQEE 357

Query: 364 CFGPVACLYKVSSLQEAIALSNDSDFGLSSSVWTNDETEATEAARSIEAGGVFINGLTAS 423
            FGPVA +++   +  AIAL+ND  FGL SSVWT+D+ E     R IE+G   +N L AS
Sbjct: 358 IFGPVAMVFRADDIDAAIALANDVPFGLGSSVWTSDQAEIDRFVRDIESGMTAVNQLLAS 417

Query: 424 FPAVPFGGLKDSGYGRELSAYGIREFVNIKTV 455
            P  PFGG+K SG+GREL  +G+ EF+N+K V
Sbjct: 418 TPEAPFGGVKLSGHGRELGPWGLHEFMNLKAV 449


Lambda     K      H
   0.317    0.132    0.386 

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: 474
Number of extensions: 14
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: 458
Length of database: 453
Length adjustment: 33
Effective length of query: 425
Effective length of database: 420
Effective search space:   178500
Effective search space used:   178500
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: 51 (24.3 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