GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4483
          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:

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