GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lctD in Pseudomonas fluorescens FW300-N2C3

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate AO356_01090 AO356_01090 glycolate oxidase subunit GlcD

Query= BRENDA::H6LBS1
         (466 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01090 AO356_01090
           glycolate oxidase subunit GlcD
          Length = 499

 Score =  219 bits (558), Expect = 2e-61
 Identities = 137/429 (31%), Positives = 217/429 (50%), Gaps = 7/429 (1%)

Query: 36  DELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIPVVVRGSGTGLVGACVPLFGGIMLET 95
           D L +  + P +++     E+V  ++K  +E N+PVV RG+GTGL G  +PL  G++L  
Sbjct: 47  DGLSAYRTTPLLVVLPRRVEQVQALLKLCHEQNVPVVARGAGTGLSGGALPLASGVLLVM 106

Query: 96  TLMNNILELDTENLTVTVEPGVLLMELSKFVEENDLFYPPDPGEKSA-TIAGNISTNAGG 154
              N IL +D +  T  ++PGV  + +S+      L+Y PDP  + A +I GN++ NAGG
Sbjct: 107 ARFNQILHIDPDARTARLQPGVRNLAISQAAAPFGLYYAPDPSSQIACSIGGNVAENAGG 166

Query: 155 MRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKNSSGYSLKDLVIGSEGTLCVITKAIL 214
           +  +KYG+T   +  L ++   GE + LG + + +S G  L  L  GSEG L VIT+  +
Sbjct: 167 VHCLKYGLTVHNLLKLEILTVEGERLTLGSESL-DSPGLDLLALFTGSEGLLGVITEVTV 225

Query: 215 KLLPLPKMTLSLLIPFENISDAAGIVPKIIKSKAIPTAIEFMERQTILFAEDFLGKKFPD 274
           KLLP P++   LL  F+++  A   V  II +  IP  +E M+   I  AEDF+   +P 
Sbjct: 226 KLLPRPQVAKVLLASFDSVDKAGRAVADIIAAGIIPGGLEMMDNLAIRAAEDFIHAGYP- 284

Query: 275 SSSNAYILLTFDGNTKEQVEAEYETVANLCLAEGAKDVYIVDTVERKDSVWSARGAFLEA 334
             + A +L   DG  +  V  + E V  +    GA +V        +   W+ R     A
Sbjct: 285 VDAEAILLCELDG-VEADVHDDCERVRQVLEQAGATEVRQARDEAERLRFWAGRKNAFPA 343

Query: 335 IKASTTEMDECDVVVPRNRIAEFIEFTHDLAKEMDVRIPSFGHAGDGNLHIYVCRDELCQ 394
           +     +    D  +PR  + E ++    L  E  +R+ +  HAGDGN+H  +  D    
Sbjct: 344 VGRLAPDYYCMDGTIPRRALPEVLQRIASLGAEYGLRVANVFHAGDGNMHPLILFD--AN 401

Query: 395 ADWEAKLAEAM-DRMYAKALTFEGLVSGEHGIGYAKRKYLLNDFGTEHLALMAGIKQTFD 453
              E + AE +  ++    +   G ++GEHG+G  K   +   F ++ L L   +K  FD
Sbjct: 402 QPGELERAETLGGKILELCVQVGGSITGEHGVGREKINQMCTQFNSDELNLFHAVKAAFD 461

Query: 454 PKNLLNPKK 462
           P+ LLNP K
Sbjct: 462 PQGLLNPGK 470


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: 549
Number of extensions: 25
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: 466
Length of database: 499
Length adjustment: 34
Effective length of query: 432
Effective length of database: 465
Effective search space:   200880
Effective search space used:   200880
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 preprint 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