GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Algiphilus aromaticivorans DG1253

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_043765410.1 U743_RS02990 aldehyde dehydrogenase family protein

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



>NCBI__GCF_000733765.1:WP_043765410.1
          Length = 508

 Score =  336 bits (862), Expect = 1e-96
 Identities = 187/484 (38%), Positives = 285/484 (58%), Gaps = 9/484 (1%)

Query: 17  YEQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWS 76
           +++  G FI+ ++VQ  S +    ++P+  + ++ +    +ED   AV+AA  AF  +WS
Sbjct: 20  FQKEYGHFIDGKWVQGASGERIPMINPANGQVLSHIQSGNAEDARRAVDAAAQAF-PAWS 78

Query: 77  TSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLM-CSKGDVALTAAYFRSCAGWTD 135
            +    R +VLY++A  +       A ++ LDNGK  M     D+ +    F   +G   
Sbjct: 79  QTPRSERQRVLYEMARRLRARMADYAMMDCLDNGKPAMEAMHFDLPMAIEQFEIFSGAPW 138

Query: 136 KIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAEST 195
            + G  I+  +T      REP+GV  QIIPWN PL+M + KL P L  G T VLK +E  
Sbjct: 139 FLHGQSIDAPNT-LGIVLREPLGVVAQIIPWNVPLIMMAAKLAPALAAGNTVVLKPSEIV 197

Query: 196 PLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAA 255
            LS L     + +   PPGVVNVV+G+GP+ G  + +HPK++KVAFTGS  T + +M+ A
Sbjct: 198 CLSVLEFFREMADL-LPPGVVNVVTGYGPSVGEALVTHPKVRKVAFTGSRPTAQKLMQYA 256

Query: 256 AESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDK 315
           +  N+   T+ELGGKS NIV +DAD+ +  +        N GEVC AGSR++V E + D 
Sbjct: 257 SV-NIIPQTMELGGKSANIVCEDADLDAAAEGAAMSTVLNKGEVCLAGSRVFVHEKVKDV 315

Query: 316 IVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNK 375
            + +F +  + +K GDP +  T +G Q S+ Q DKI+ Y+++G++EGA +  GG +    
Sbjct: 316 FLDKFTSLLKRVKAGDPREPTTQIGPQVSKAQYDKIMGYLELGQQEGAKLAAGGRKAAPA 375

Query: 376 GY----FIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHT 431
           G+    FI+PT+F DV    +I ++EIFGPV  +  F+  +EV+ +ANDS YGL  G+ T
Sbjct: 376 GFEDGLFIEPTVFFDVDNSMRIAQEEIFGPVSCVIGFRDDDEVVRMANDSVYGLGGGLWT 435

Query: 432 TNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRI 491
            +LS A  ++  + +GT+WVN Y +F   +P GGY QSG GRE   E +++YT  K+V I
Sbjct: 436 KDLSRAHRIARALETGTVWVNRYYNFLGGMPIGGYKQSGFGREFAAEVMNHYTLTKSVII 495

Query: 492 GLSQ 495
            L++
Sbjct: 496 NLAE 499


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: 624
Number of extensions: 33
Number of successful extensions: 6
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: 508
Length adjustment: 34
Effective length of query: 461
Effective length of database: 474
Effective search space:   218514
Effective search space used:   218514
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