GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Korea:Ga0059261_1006 Ga0059261_1006
           NAD-dependent aldehyde dehydrogenases
          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 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