GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctD in Pseudomonas fluorescens FW300-N2E2

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate Pf6N2E2_1497 D-2-hydroxyglutarate dehydrogenase

Query= BRENDA::H6LBS1
         (466 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1497
          Length = 474

 Score =  201 bits (512), Expect = 3e-56
 Identities = 152/465 (32%), Positives = 224/465 (48%), Gaps = 14/465 (3%)

Query: 13  AIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIPVV 72
           A++ L+ A  V  G E    +  D+ G         +   STEEV+ +++     + PVV
Sbjct: 8   ALQALVGARHVQDGEEAAP-YLTDKQGRYVGQVIAAVHPASTEEVAAVVRACAAADTPVV 66

Query: 73  VRGSGTGLVGACVPLFGG--IMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEEND 130
           V+G  TGL+G   P   G  ++L    MN +  +DT+N T+TVE G +L  +     E  
Sbjct: 67  VQGGNTGLMGGATPDASGRAVLLLLDRMNRVRAVDTDNDTLTVEAGCILQTVQDVAREAG 126

Query: 131 LFYPPDPG-EKSATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKN 189
             +P   G E S T+ GN+ TNAGG   ++YG TR+   GL VV A GEI      + K+
Sbjct: 127 RLFPLSLGAEGSCTLGGNLGTNAGGTAVLRYGNTRELTLGLEVVTAQGEIWNGLRGLRKD 186

Query: 190 SSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKS-KA 248
           ++GY L+DL IGSEGTL +IT A LKL PLPK   + L+ F+++  A  ++        A
Sbjct: 187 NTGYDLRDLFIGSEGTLGIITAATLKLFPLPKARATALLAFDSLEQAVALLSHARAGFGA 246

Query: 249 IPTAIEFMERQTI-LFAEDFLGKKFPDSSSN---AYILLTFDGNTKEQVEAEYETVANLC 304
             TA E +  + + L  E F     P S +      +L   D +++ +    +E V    
Sbjct: 247 SLTAFELLSAECLALLREQFPDGPRPFSGTRWPWFALLELSDNHSESRAREVFEQVLGEA 306

Query: 305 LAEG-AKDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAEFIEFTHD 363
             +    D  I + + +  + W  R    +A K +   M   D+ VP +++  F+  T  
Sbjct: 307 FEQQLLADALIAENLVQSQAFWQLRENMSDAQKRAGRNMKH-DISVPISQVVAFVAHTDA 365

Query: 364 LAKE--MDVRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRM-YAKALTFEGLVS 420
           L ++    VR  +FGH GDGNLH  V        D       A+ ++ +  A    G +S
Sbjct: 366 LLQQHFPGVRHYTFGHLGDGNLHYNVAHPLDSTVDAHMAHYPALSQLVHDSAHAHGGSIS 425

Query: 421 GEHGIGYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKVCQ 465
            EHGIG  K   L        L LM  IKQ  DP+NLLNP KV +
Sbjct: 426 AEHGIGQRKVNVLGRYKSAVELDLMHRIKQALDPRNLLNPGKVLE 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: 435
Number of extensions: 19
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: 474
Length adjustment: 33
Effective length of query: 433
Effective length of database: 441
Effective search space:   190953
Effective search space used:   190953
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: 51 (24.3 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