GapMind for catabolism of small carbon sources

 

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

Align Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized)
to candidate 3608345 Dshi_1747 methylmalonate-semialdehyde dehydrogenase (RefSeq)

Query= SwissProt::D4GP41
         (482 letters)



>lcl|FitnessBrowser__Dino:3608345 Dshi_1747
           methylmalonate-semialdehyde dehydrogenase (RefSeq)
          Length = 499

 Score =  284 bits (727), Expect = 4e-81
 Identities = 166/476 (34%), Positives = 253/476 (53%), Gaps = 6/476 (1%)

Query: 7   NYVNGEWVTSETGETTEVTNPANPSEVVAAYQHSNENDAAAAVDAAVAAEDEWRNTPGPE 66
           +++NG+ V   +G   +V NPA   EV A    ++  +  AAV AA AA+  W  T    
Sbjct: 6   HFINGKRVAGTSGRFADVMNPAT-GEVQARVPLASPEELDAAVAAAAAAQPAWAATNPQR 64

Query: 67  RGRILREAGTLLAQRKDELTEILTAEEGKARPEAAGEVQRAIDIFHYFSSKAADLGGTKK 126
           R R+L E   LL +  D+L E L+ E GK  P+A G+V R +++  +       L G   
Sbjct: 65  RARVLMEFVRLLNRDMDKLAEALSREHGKTLPDAKGDVVRGLEVVEFCIGAPHLLKGEFT 124

Query: 127 GASGPNTNLYTRQEPVGVAALITPWNYPIAIPAWKLAPALAAGNTVVLKPASIAPGVVIE 186
            ++GP  ++Y+ ++ +GV A ITP+N+P  IP WK+APALA GN  +LKP+   P V + 
Sbjct: 125 DSAGPGIDMYSMRQALGVVAGITPFNFPAMIPMWKMAPALACGNAFILKPSERDPSVPLM 184

Query: 187 IARALDEAGLPDGVLNVVTGPGSSVGSEFIGNEGTDLVSFTGSSQVGEMVYEQATDAGKR 246
           +A  + EAGLPDG+L V+ G   +V +  + N+    + F GS+ + E +Y +    GKR
Sbjct: 185 LAELMTEAGLPDGLLQVINGDKGAVDA-ILDNDTIQAIGFVGSTPIAEYIYSRGCANGKR 243

Query: 247 VQTELGGKNPTLVADSANPAEAADIVANGGFGTTGQSCTACSRAI-VHEDVYDDFVAELV 305
           VQ   G KN  ++   A+  +AAD +   G+G  G+ C A S A+ V E+  D  + +LV
Sbjct: 244 VQCFGGAKNHMIIMPDADLDQAADALVGAGYGAAGERCMAISVAVPVGEETADRLIEKLV 303

Query: 306 DRAESLDVGP---GTDHEMGPQVSESELSSTLEYIDIAEAEGATLVAGGGVPEGEAVETG 362
            R E+L VGP   GTD + GP V+ +  ++    +     +GA LV  G     +  E G
Sbjct: 304 PRVEALKVGPYTSGTDVDYGPVVTAAAKANIERLVQSGVDQGAKLVVDGRDFSLQGYENG 363

Query: 363 HFVEPTVFTDVDPDMRIAQEEVFGPVVAVIEVSDFDEGLAVANDVDYGLSASIVTDDHTE 422
            FV P +F +V  +M I + E+FGPV+  +    ++E L +A D +YG   +I T D   
Sbjct: 364 FFVGPHLFDNVSKEMDIYRTEIFGPVLCTVRAKSYEEALGLAMDHEYGNGTAIFTRDGDA 423

Query: 423 ANRFVDEVEAGVVKVNDKTTGLELHVPFGGFKRSSSETWREQGDAGLDFYTIEKTV 478
           A  F + +  G+V +N        +  FGG+K+S      + G     FYT  KTV
Sbjct: 424 ARDFANRINIGMVGINVPIPVPLAYHTFGGWKKSGFGDLNQHGPDAFRFYTRTKTV 479


Lambda     K      H
   0.310    0.130    0.370 

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: 588
Number of extensions: 30
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: 482
Length of database: 499
Length adjustment: 34
Effective length of query: 448
Effective length of database: 465
Effective search space:   208320
Effective search space used:   208320
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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