GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lctD in Acidovorax sp. GW101-3H11

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate Ac3H11_4483 Glycolate dehydrogenase (EC 1.1.99.14), subunit GlcD

Query= BRENDA::H6LBS1
         (466 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4483 Glycolate
           dehydrogenase (EC 1.1.99.14), subunit GlcD
          Length = 504

 Score =  224 bits (570), Expect = 7e-63
 Identities = 142/458 (31%), Positives = 230/458 (50%), Gaps = 5/458 (1%)

Query: 7   EASDIAAIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYE 66
           +A  + A+ + +PA  +   +E    +  D L +    P V+    + +EV  +++  + 
Sbjct: 23  QAEVVQALGQAVPAHALLWHSEDTTPYECDGLTAYRQRPLVVCLPETYDEVQAVLRACHR 82

Query: 67  HNIPVVVRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFV 126
             +PVV RG+GTGL G  +P   G+ L     N IL L  E+ T  V+ GV  + +S+  
Sbjct: 83  LQVPVVARGAGTGLSGGAMPHAMGVTLSLAKFNRILNLSPESRTAVVQSGVRNLAISEAA 142

Query: 127 EENDLFYPPDPGEKSA-TIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGK 185
             ++L+Y PDP  + A TI GN++ N+GG+  +KYG+T   V  +      GE +E G +
Sbjct: 143 APHNLYYAPDPSSQIACTIGGNVAENSGGVHCLKYGLTVHNVLKVKGFTVEGEPVEFGSE 202

Query: 186 IVKNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIK 245
            + +S GY L   VIGSEG L VIT+  ++L+P P++   ++  F+++  A   V  +I 
Sbjct: 203 AL-DSPGYDLLAAVIGSEGMLAVITEVTVRLIPKPQLARCIMASFDDVRKAGDAVAAVIA 261

Query: 246 SKAIPTAIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCL 305
           +  IP  +E M++      EDF+   + D ++ A +L   DG T E+VE E   ++ +  
Sbjct: 262 AGIIPAGLEMMDKPMTAAVEDFVHAGY-DLTAEAILLCESDG-TPEEVEEEIGRMSEVLR 319

Query: 306 AEGAKDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAEFIEFTHDLA 365
           A GA  + +      +   WS R     A    + +    D  +PR R+A+ +    ++ 
Sbjct: 320 AAGATAISVSRDEAERLRFWSGRKNAFPASGRISPDYMCMDSTIPRKRLADILLAIQEME 379

Query: 366 KEMDVRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRMYAKALTFEGLVSGEHGI 425
           K+  +R  +  HAGDGNLH  +  D    AD   +       +   ++   G V+GEHG+
Sbjct: 380 KKYQLRCANVFHAGDGNLHPLILFD-ANDADQLHRCELFGADILETSVAMGGTVTGEHGV 438

Query: 426 GYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463
           G  K   +   F  E  A M G+K  FDP  LLNP KV
Sbjct: 439 GVEKLNSMCVQFTAEENAQMFGLKHAFDPAGLLNPGKV 476


Lambda     K      H
   0.318    0.136    0.388 

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: 526
Number of extensions: 33
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: 466
Length of database: 504
Length adjustment: 34
Effective length of query: 432
Effective length of database: 470
Effective search space:   203040
Effective search space used:   203040
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: 52 (24.6 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 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