GapMind for catabolism of small carbon sources

 

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

Align gluconolactonase subunit (EC 3.1.1.17) (characterized)
to candidate Ac3H11_138 Gluconolactonase

Query= metacyc::MONOMER-13276
         (356 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_138
          Length = 307

 Score = 87.0 bits (214), Expect = 6e-22
 Identities = 81/272 (29%), Positives = 126/272 (46%), Gaps = 35/272 (12%)

Query: 76  EGPVWVKNGNFLLFSDPPANIMRKWTPDAGVSIFLKPSGHAEPIPAGQFREPGSNGMKVG 135
           EGPV+   GN  +   P   I R           + P G A  + A    EP  NGMK  
Sbjct: 45  EGPVFDGVGNLYVTDIPWGRIFR-----------IDPQG-AWTLVAEYDGEP--NGMKFM 90

Query: 136 PDGKIWVADSGTRAIMKVDPVTRQRSVVVDNYKGKRFNSPNDLFFSKSGAVYFTDPPYGL 195
             G + + D     +M++D  T   +  ++    +RF   NDL F   G +YFTD   G 
Sbjct: 91  DAGTLLITDY-KNGLMRLDIATGGVTPYLERRNSERFKGVNDLIFDADGNLYFTDQ--GQ 147

Query: 196 TNLDESDIKEMNYNGVFRLSPDGRLDLIEAGLSRPNGLALSPDETKLYVSNSDRASPNIW 255
           + L +   +      ++RL P+G+LDL+ A +  PNG+ALSPD   LY++ +      +W
Sbjct: 148 SGLHDPSGR------LYRLRPNGQLDLLLANVPSPNGVALSPDGRVLYLAAT--RGNCVW 199

Query: 256 VYSLDSNGLPTSRTLLRNFRKEYFDQGLAGLPDGMNIDKQGNLFASAPGGIYIFAPD--G 313
              L  +G   S   +  F   +   G    PDG+ +D  G L  + PG  Y++  +   
Sbjct: 200 RVPLLPDG---SVAKVGQFFTSHGPSG----PDGLAVDTSGRLLVANPGLGYVWVLNHRA 252

Query: 314 ECLGLISGNPGQPLSNCCF-GEKGQTLFISAS 344
           E + ++ G  G   +N  F G+ GQT+F++ S
Sbjct: 253 EPVLVLRGPAGASTTNLAFGGQGGQTVFVTDS 284


Lambda     K      H
   0.317    0.135    0.409 

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: 479
Number of extensions: 48
Number of successful extensions: 6
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: 356
Length of database: 307
Length adjustment: 28
Effective length of query: 328
Effective length of database: 279
Effective search space:    91512
Effective search space used:    91512
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 (21.6 bits)
S2: 49 (23.5 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