GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Dinoroseobacter shibae DFL-12

Align Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)
to candidate 3608023 Dshi_1430 aldehyde dehydrogenase (RefSeq)

Query= SwissProt::O34660
         (495 letters)



>lcl|FitnessBrowser__Dino:3608023 Dshi_1430 aldehyde dehydrogenase
           (RefSeq)
          Length = 487

 Score =  348 bits (893), Expect = e-100
 Identities = 192/459 (41%), Positives = 270/459 (58%), Gaps = 6/459 (1%)

Query: 38  DTPNPATGETLMTLYEAQAADVDKAVKAARKAFDQGEWRTMSPASRSRLMYKLADLMEEH 97
           D  NPATGE +  +      +VD+AV AAR+AF+ GEW  ++   R RL++KL + +  H
Sbjct: 29  DVTNPATGEKIAQIPACGPDEVDRAVTAARRAFEDGEWSRLTAVDRGRLLHKLGEAITAH 88

Query: 98  KTELAQLETLDNGKPINETTNGDIPLAIEHMRYYAGWCTKITGQTIPVSGAYFNYTRHEP 157
             ELA+ E  D GKP+ +    D+  A  +  YY     K+ G+TIP    Y   T  EP
Sbjct: 89  GQELAEWEAKDTGKPLAQA-RADMVAAARYFEYYGAAADKVHGETIPFLSGYQVQTIFEP 147

Query: 158 VGVVGQIIPWNFPLLMAMWKMGAALATGCTIVLKPAEQTPLSALYLAELIDQAGFPAGVI 217
            GV G IIPWN+P  M       ALA G  +VLKPAE   L+ L +AEL  + GFP G I
Sbjct: 148 YGVTGHIIPWNYPAQMFGRSCAPALAMGNAVVLKPAEDACLTPLRIAELALEVGFPGGAI 207

Query: 218 NIIPGFGEDAGEALTNHEAVDKIAFTGSTEIGKKIMSTAAKSIKRVTLELGGKSPNILLP 277
           N++ G+G++AG ALT H  VD ++FTGS E+G  I + AA++    TLELGGKSP I+  
Sbjct: 208 NVVTGYGQEAGAALTTHRDVDFLSFTGSPEVGVMIQTAAARNHIGCTLELGGKSPQIVFA 267

Query: 278 DANLKKAIPGALNGVMFNQGQVCCAGSRVFIHKDQYDEVVDEMASYAESLRQGAGLHKDT 337
           DA+L  AIP  LNG++ N GQ C AGSR  I +D +D V+  + +  E+L   A   ++ 
Sbjct: 268 DADLDAAIPVLLNGIVQNGGQTCSAGSRALIQRDIFDAVLARLKAGFEAL-TAAPWQENG 326

Query: 338 QIGPLVSKEQHERVLSYIQKGKDEGAKAVTGG---SCPFEAGYFVAPTVFANVEDEMTIA 394
            +GPL+S +Q  RV  +I +G    A  V  G   +   EAG FVAP +F  V +   +A
Sbjct: 327 NLGPLISHKQKRRVEGFIAEGGGADAPLVARGRIAASASEAGSFVAPALFGPVIEGHVLA 386

Query: 395 KEEIFGPVLTAIPYETVDEVIERANHSEYGLAAGLWTENVKQAHYIADRLQAGTVWVNCY 454
           +EE+FGPVL+ IP+    + I  AN ++YGL A +W+ +  +   +A RL+ G V++NCY
Sbjct: 387 REEVFGPVLSCIPFTDEADAIRIANATDYGLVASVWSADGGRQMRLAKRLRVGQVFLNCY 446

Query: 455 NVFDAAS-PFGGYKQSGLGREMGSYALDNYTEVKSVWVN 492
                   PFGG ++SG GRE G  AL  ++++K+V  N
Sbjct: 447 GAGGGIELPFGGMRKSGHGREKGFAALHEFSQIKTVVQN 485


Lambda     K      H
   0.316    0.133    0.391 

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: 618
Number of extensions: 34
Number of successful extensions: 5
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: 487
Length adjustment: 34
Effective length of query: 461
Effective length of database: 453
Effective search space:   208833
Effective search space used:   208833
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, 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