GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Acidovorax sp. GW101-3H11

Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate Ac3H11_2359 Butyryl-CoA dehydrogenase (EC 1.3.99.2)

Query= metacyc::MONOMER-11693
         (386 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2359
          Length = 388

 Score =  245 bits (625), Expect = 2e-69
 Identities = 147/386 (38%), Positives = 218/386 (56%), Gaps = 12/386 (3%)

Query: 1   MDHRLTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYG 60
           MD  LT E     +T  +FA    AP    + E   FP E + + G +G  GL  PE  G
Sbjct: 1   MDFELTEEQRAFAQTARDFAQAEFAPHAAHWDEEGIFPKEAIAKAGELGFCGLYAPEAAG 60

Query: 61  GMGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKA---EWLPRLCSG 117
           G+    L   +  EE+A VD S      A +++  M   + GT A  A    W P L +G
Sbjct: 61  GLALPRLDATLVFEEMAAVDPSTT----AFITIHNMATWMLGTWATPAVRDHWGPLLTTG 116

Query: 118 EILGAFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTG 177
           E L ++ LTEP  GSDA + +T A L    NE+VING K FI+ +G+  T ++ + A TG
Sbjct: 117 EKLASYCLTEPGAGSDAASLKTRAEL--VGNEYVINGAKAFISGAGS--TDVLVLMARTG 172

Query: 178 RKPDGKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGY 237
               G   IS+  VP+  PG +      K+GWN+  TR +SF +VR+PA +LLG +G G+
Sbjct: 173 DAQSGASGISAFAVPADAPGISYGKKEQKMGWNSQPTRTISFDNVRIPADHLLGREGEGF 232

Query: 238 AQFLRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKA 297
              ++ LD GRI I+  + G AQG ++ + +Y  +R  FG+ I ++QA+QFK+ADM  + 
Sbjct: 233 KIAMKGLDGGRINIATCSVGAAQGALNAAQQYMQDRKQFGKPIASFQALQFKLADMATEL 292

Query: 298 HMARVGWRDAASRLVAG-EPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVAR 356
             AR   R AAS+L AG        A+AK +++        +A Q+HGGYG++ EYP+ R
Sbjct: 293 VAARQMVRLAASKLDAGARDASTYCAMAKRFATDAGFTVINDALQLHGGYGYIREYPLER 352

Query: 357 MWRDSKILEIGEGTSEVQRMLIAREL 382
           + RD+++ +I EGT+E+ R++IAR +
Sbjct: 353 LLRDARVHQILEGTNEIMRVIIARRM 378


Lambda     K      H
   0.318    0.136    0.402 

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: 380
Number of extensions: 19
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: 386
Length of database: 388
Length adjustment: 30
Effective length of query: 356
Effective length of database: 358
Effective search space:   127448
Effective search space used:   127448
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