GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldA in Paraburkholderia bryophila 376MFSha3.1

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate H281DRAFT_03016 H281DRAFT_03016 aldehyde dehydrogenase (acceptor)

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



>lcl|FitnessBrowser__Burk376:H281DRAFT_03016 H281DRAFT_03016
           aldehyde dehydrogenase (acceptor)
          Length = 483

 Score =  395 bits (1016), Expect = e-114
 Identities = 194/456 (42%), Positives = 287/456 (62%), Gaps = 3/456 (0%)

Query: 41  VSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVRMKVLYKLADLIDEHADT 100
           ++P+TEE I  V +  + D+D AV AA AA    W+      R ++L +LA L+  + D 
Sbjct: 30  INPATEEPIAHVAQGSAADVDTAVRAARAAL-KVWNGIKAAERGRILSRLAGLMRANLDE 88

Query: 101 LAHIEALDNGKSLMC-SKGDVALTAAYFRSCAGWTDKIKGSVIETGDTHFNYTRREPIGV 159
           LA +E+LD GK +    + DV          AGW DKI G V+        YT REP+GV
Sbjct: 89  LAALESLDAGKPIAAVMRQDVPAAIDTLEYYAGWCDKINGQVVPVRPDALTYTLREPVGV 148

Query: 160 CGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPPGVVNVV 219
              I+PWNFPL++  WK+ P L  GCT ++K AE TPLSAL +  L  EAG PPGV+N+V
Sbjct: 149 VAAIVPWNFPLMIGMWKIAPALACGCTLIVKPAEITPLSALRIGELALEAGVPPGVLNIV 208

Query: 220 SGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKKVTLELGGKSPNIVFDDA 279
           +G G   G  + +HP + KV FTGS + GR I++ AA  N K+VTLELGGKS N++F DA
Sbjct: 209 TGKGRVVGDALVAHPGVDKVTFTGSPSVGRGILQGAA-GNFKRVTLELGGKSANLIFPDA 267

Query: 280 DVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKNAAESLKIGDPFKEDTFM 339
           ++ + ++   +GIF+NTG+VC AGSRI     +YD++V      A+S+K+GDP   +T M
Sbjct: 268 NLDNAVRAAASGIFFNTGQVCSAGSRILAHRDVYDEVVERLAARAKSIKVGDPSSRETSM 327

Query: 340 GAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYFIKPTIFGDVKEDHQIVRDEIF 399
           G   S  Q+  +L Y+D G+ EGA+++TGG R G +G+F++PT+F +V+ + +I ++EIF
Sbjct: 328 GPLISAAQMKTVLGYVDAGRSEGASLVTGGGRIGERGFFVEPTVFANVEHEMRISQEEIF 387

Query: 400 GPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHP 459
           GPV ++ +F    + I +AN + Y LAAGV + ++     V+  + +GT+W+NTY     
Sbjct: 388 GPVASVIRFNDEADAIRIANGTLYSLAAGVWSADIGRVHRVARDLRAGTVWINTYGYTDV 447

Query: 460 MVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGLSQ 495
            +P+GG   SG GRE G+ A++N+T+ KAV + + Q
Sbjct: 448 RLPWGGSGDSGFGREHGDVAIENFTEPKAVWLAIDQ 483


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: 610
Number of extensions: 25
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: 495
Length of database: 483
Length adjustment: 34
Effective length of query: 461
Effective length of database: 449
Effective search space:   206989
Effective search space used:   206989
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 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, the preprint on GapMind for carbon sources, 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