GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Paraburkholderia bryophila 376MFSha3.1

Align Succinate--hydroxymethylglutarate CoA-transferase; Dermal papilla-derived protein 13; SuccinylCoA:glutarate-CoA transferase; EC 2.8.3.13 (characterized)
to candidate H281DRAFT_03740 H281DRAFT_03740 Crotonobetainyl-CoA:carnitine CoA-transferase CaiB

Query= SwissProt::Q9HAC7
         (445 letters)



>FitnessBrowser__Burk376:H281DRAFT_03740
          Length = 388

 Score =  278 bits (710), Expect = 3e-79
 Identities = 143/377 (37%), Positives = 228/377 (60%), Gaps = 2/377 (0%)

Query: 47  PLEGVKILDLTRVLAGPFATMNLGDLGAEVIKVERPGAGDDTR-TWGPPFVGTESTYYLS 105
           PL+G+++LD+++V+AGPFA M L DLGA+VIKVE P  GD TR + G    G +S  +L+
Sbjct: 8   PLQGIRVLDVSQVMAGPFACMMLADLGADVIKVE-PPEGDQTRGSMGFKMKGPDSMGFLN 66

Query: 106 VNRNKKSIAVNIKDPKGVKIIKELAAVCDVFVENYVPGKLSAMGLGYEDIDEIAPHIIYC 165
           +NRNK+S+ +++K  +G ++  +LA   DV VENY PG +  + + YE I  I P I+Y 
Sbjct: 67  LNRNKRSVTLDLKSDEGRELFYKLAKTADVIVENYRPGVVQRLRIDYESIKAINPKIVYA 126

Query: 166 SITGYGQTGPISQRAGYDAVASAVSGLMHITGPENGDPVRPGVAMTDLATGLYAYGAIMA 225
           SI+G+GQ+GP + R G+D +A A+SG+M +TG + G PV+ GV + D+   ++A   +++
Sbjct: 127 SISGFGQSGPWASRPGFDLMAQAMSGVMSVTGYKGGKPVKAGVPVADIGCAMFAVYGLLS 186

Query: 226 GLIQKYKTGKGLFIDCNLLSSQVACLSHIAANYLIGQKEAKRWGTAHGSIVPYQAFKTKD 285
             I   KTG+G  ID +L  S +A      ++Y          GT++    PYQA K +D
Sbjct: 187 AYIGAQKTGEGQHIDASLFDSIMAFSIWDMSDYWGTGVPPTPLGTSNKMSAPYQAVKARD 246

Query: 286 GYIVVGAGNNQQFATVCKILDLPELIDNSKYKTNHLRVHNRKELIKILSERFEEELTSKW 345
           GY V+GA N + +  +C +L+ P+LID++ Y    LR+ NR+ +I++L + F +  +++W
Sbjct: 247 GYFVMGATNQKLWTKLCHVLERPDLIDHADYANVSLRLKNREAMIEVLEQEFGKRDSNEW 306

Query: 346 LYLFEGSGVPYGPINNMKNVFAEPQVLHNGLVMEMEHPTVGKISVPGPAVRYSKFKMSEA 405
           + +   +G+P GPI +    F      H  + ME++HP  GK+   G  V+      +  
Sbjct: 307 VDILLAAGIPAGPILSYPEAFESDHARHRNMCMEIDHPNEGKVKNIGFPVKLLGTPPTVR 366

Query: 406 RPPPLLGQHTTHILKEV 422
           R PPLLG+H   I  E+
Sbjct: 367 RHPPLLGEHNEEIFAEI 383


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: 445
Number of extensions: 23
Number of successful extensions: 2
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: 388
Length adjustment: 31
Effective length of query: 414
Effective length of database: 357
Effective search space:   147798
Effective search space used:   147798
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