GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Lentibacillus jeotgali Grbi

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_010531933.1 ON01_RS15200 aldehyde dehydrogenase family protein

Query= BRENDA::P05091
         (517 letters)



>NCBI__GCF_000224785.1:WP_010531933.1
          Length = 480

 Score =  360 bits (924), Expect = e-104
 Identities = 195/477 (40%), Positives = 284/477 (59%), Gaps = 8/477 (1%)

Query: 39  IFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDA 98
           ++IN +W D+  ++T    NPSTGEV+  +  G  +DVDKAV+AA+ +F +   WRR+  
Sbjct: 6   MYINGKWEDSHDKETINVNNPSTGEVMTTIPRGKNDDVDKAVRAAKDSF-VSEEWRRVKP 64

Query: 99  SHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHG 158
             RGR+L  +   ++ +R  LA LET+D GKP    Y  D+D  ++   +Y G ADK  G
Sbjct: 65  FERGRILCEVVAQLKENRDELARLETMDVGKPLTQGY-ADIDAAIRYFEFYGGAADKVMG 123

Query: 159 KTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTA 218
            TIPI+     Y   EP+GV   I+PWN+P+ + +  +  A+A GN VV+K AE TPLTA
Sbjct: 124 DTIPIEDGLIDYVIREPIGVTAHIVPWNYPIQILSRSVAAAIAMGNTVVVKSAEDTPLTA 183

Query: 219 LYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSN 278
             +A    +   P GV N V G+G  AGAA++SH  ++ + FTGS   G  +  AA +SN
Sbjct: 184 AKIAEYFDQTDLPEGVFNHVTGYGYEAGAALSSHPLINHLTFTGSVGTGTAVANAA-TSN 242

Query: 279 LKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVER 338
           +  VTLELGGKSPNI+ SD D+D AVE    A+  N GQ C AGSR  ++E     F+++
Sbjct: 243 VVPVTLELGGKSPNIVFSDCDVDKAVEGVVKAIIQNAGQTCSAGSRLLIEESFKQTFLDK 302

Query: 339 SVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADR---G 395
            V + K+  VG   D     GP +++ QF +IL +I+  +QEG  L  G  +  ++    
Sbjct: 303 LVNKFKTLSVGPAIDDH-NLGPILNQKQFDRILEFISLAEQEGTVLTGGKRVKYEQYENA 361

Query: 396 YFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDK 455
            +++PT+  ++      A+EEIFGPV+ +  FK  +E +  AN++ YGL   ++TKD++K
Sbjct: 362 CYLEPTIIDNLSLNSKAAQEEIFGPVLSVFTFKNEQEAIDIANSTDYGLVTGIWTKDINK 421

Query: 456 ANYLSQALQAGTVWVNCYDVFGA-QSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVK 511
           A+ L   + +G V++N Y   G  Q PFGGYK SG GRE G   L  YT+VK V +K
Sbjct: 422 AHLLMSRIDSGQVFINNYGAGGGIQMPFGGYKKSGFGREKGWIALYNYTQVKNVAIK 478


Lambda     K      H
   0.319    0.136    0.409 

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: 625
Number of extensions: 25
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: 517
Length of database: 480
Length adjustment: 34
Effective length of query: 483
Effective length of database: 446
Effective search space:   215418
Effective search space used:   215418
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 (21.8 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