GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo5_N2C3_1:AO356_01090
          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:

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