GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Dyella japonica UNC79MFTsu3.2

Align Succinate--hydroxymethylglutarate CoA-transferase; Dermal papilla-derived protein 13; SuccinylCoA:glutarate-CoA transferase; EC 2.8.3.13 (characterized)
to candidate N515DRAFT_3223 N515DRAFT_3223 Crotonobetainyl-CoA:carnitine CoA-transferase CaiB

Query= SwissProt::Q9HAC7
         (445 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3223
          Length = 384

 Score =  191 bits (485), Expect = 3e-53
 Identities = 114/373 (30%), Positives = 194/373 (52%), Gaps = 8/373 (2%)

Query: 47  PLEGVKILDLTRVLAGPFATMNLGDLGAEVIKVERPGAGDDTRTWGPPFVGTESTYYLSV 106
           PL G+++LDL+  +AGP+    L D GA+V+K+E PG GD+ R + P  + +ES  +L V
Sbjct: 15  PLHGIRVLDLSAYIAGPYGCTLLADQGADVLKIEPPG-GDNLRQY-PSTLPSESRAFLGV 72

Query: 107 NRNKKSIAVNIKDPKGVKIIKELAAVCDVFVENYVPGKLSAMGLGYEDIDEIAPHIIYCS 166
           NR+K+ + +++K+P    ++  L    DV V N+ P     +G+ ++ +  I P +IYC+
Sbjct: 73  NRSKRGMVLDLKNPADHAVLLRLVRDADVLVHNFRPNVPKRLGIDFDQLTAINPRLIYCA 132

Query: 167 ITGYGQTGPISQRAGYDAVASAVSGLMHITGPENGDP-VRPGVAMTDLATGLYAYGAIMA 225
           +TGYG++GP+  +AGYD V   ++G+  + G   G P +  G  +   A  L A G + +
Sbjct: 133 VTGYGESGPMRDKAGYDQVLQTMTGMCALQGKRGGPPEIIYGSVVDYYAAALLAAG-VSS 191

Query: 226 GLIQKYKTGKGLFIDCNLLSSQVACLSHIAANYLIGQKEAKRWGTAHGSIVPYQAFKTKD 285
            L ++ ++G G F+  +LL    A L+  +A  +    E+   G    S        T D
Sbjct: 192 ALYERERSGLGQFVGVSLLR---AALTMQSARLIWADGESLDIGRDMRSGGVTGIHPTAD 248

Query: 286 GYIVVGAGNNQQFATVCKILDLPELIDNSKYKTNHLRVHNRKELIKILSERFEEELTSKW 345
           G+I + A   + +  +C+   L  L ++ +Y T   R  +  E++  L E         W
Sbjct: 249 GHIYISANTPRFWRALCEKTGLHALAEDPRYDTVRKRAEHAAEILPQLHEALAARPAMAW 308

Query: 346 LYLFEGSGVPYGPINNMKNVFAEPQVLHNGLVMEMEHPTVGKISVPGPAVRYSKFKMSEA 405
             LF G  VP      ++++F  PQVL  G+V  +EHP VG+      ++++ +    E 
Sbjct: 309 EALF-GDEVPSAAARRIEDMFEHPQVLAEGIVGTIEHPVVGRYHGVAQSIKFGRTPGPEP 367

Query: 406 RPPPLLGQHTTHI 418
              P+LGQHT  +
Sbjct: 368 FAAPMLGQHTDEV 380


Lambda     K      H
   0.318    0.137    0.410 

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: 429
Number of extensions: 22
Number of successful extensions: 4
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: 445
Length of database: 384
Length adjustment: 31
Effective length of query: 414
Effective length of database: 353
Effective search space:   146142
Effective search space used:   146142
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 (21.7 bits)
S2: 50 (23.9 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