GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dino:3608345
          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:

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