GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dino:3608023
          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 (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