GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Pontimonas salivibrio CL-TW6

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_104913707.1 C3B54_RS06115 gamma-aminobutyraldehyde dehydrogenase

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



>NCBI__GCF_002950575.1:WP_104913707.1
          Length = 478

 Score =  313 bits (802), Expect = 8e-90
 Identities = 177/469 (37%), Positives = 274/469 (58%), Gaps = 8/469 (1%)

Query: 24  FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83
           FIN ++V SK  +T   V P+TEE       + + D+DDA +AA+ AF   WS + P  R
Sbjct: 9   FINGQYVDSKGSETIPLVDPATEEVYAHSPISSAADVDDAYQAASKAFEG-WSETTPAER 67

Query: 84  MKVLYKLADLIDEHADTLAHIEALDNGKS-LMCSKGDVALTAAYFRSCAGWTDKIKG-SV 141
              L+++AD +++  +  A +E+ D GK      + +++L+    R  AG    ++G S 
Sbjct: 68  QLALFRIADELEKRGEEFADLESQDAGKPRASLVEDEISLSVDQIRFFAGAARNLEGKSA 127

Query: 142 IETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALY 201
            E    H ++ RREPIGV GQ+ PWN+PL MA WK  P +  G TTVLK +++TP S L 
Sbjct: 128 GEYMKDHTSFIRREPIGVVGQVAPWNYPLNMAVWKFAPAVAAGNTTVLKPSDTTPQSTLL 187

Query: 202 LASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLK 261
           LA +      P GVVNV++G   T GA I  H   + V+ TGS   G  + KAAA ++LK
Sbjct: 188 LAEICA-MHLPEGVVNVITGDRTTGGAMID-HKIPEMVSITGSVRAGLEVAKAAA-TDLK 244

Query: 262 KVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFK 321
           +V LELGGK+P IVFDDAD+ S I+ +    ++N G+ C A +R+ V E I+D+ ++E K
Sbjct: 245 RVHLELGGKAPVIVFDDADIPSAIEGIGIAGYFNAGQDCTAATRVVVHESIHDEFIAELK 304

Query: 322 N-AAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYFIK 380
              A ++  G P   +TF G   +  Q+D+++  +       +TV  GG R G +GYFI+
Sbjct: 305 KWVAANVTTGLPSDPNTFYGPVNNANQMDRVMGILG-ELPSHSTVEAGGVRQGERGYFIE 363

Query: 381 PTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISV 440
           PTI   +K++   ++ EIFGPV+T+  F+T EE + +AN   YGL++ V T + + A+  
Sbjct: 364 PTIVSGLKQNDAAIQTEIFGPVITVQPFRTEEEAMTMANGVPYGLSSSVWTKDHARAMRF 423

Query: 441 SNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV 489
           +  ++ G +W+N +      +P GG+  SG G+++ +   + YT+VK V
Sbjct: 424 AKGLDFGAVWINCHIPLVAEMPHGGFKHSGHGKDLSQYGFEEYTRVKHV 472


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: 572
Number of extensions: 33
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: 478
Length adjustment: 34
Effective length of query: 461
Effective length of database: 444
Effective search space:   204684
Effective search space used:   204684
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