GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Burk376:H281DRAFT_03740 H281DRAFT_03740
           Crotonobetainyl-CoA:carnitine CoA-transferase CaiB
          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.

Links

Downloads

Related tools

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