GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lctD in Sphingomonas koreensis DSMZ 15582

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate Ga0059261_1691 Ga0059261_1691 FAD/FMN-containing dehydrogenases

Query= BRENDA::H6LBS1
         (466 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_1691 Ga0059261_1691
           FAD/FMN-containing dehydrogenases
          Length = 484

 Score =  172 bits (437), Expect = 2e-47
 Identities = 134/466 (28%), Positives = 223/466 (47%), Gaps = 11/466 (2%)

Query: 11  IAAIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIP 70
           ++A+ E + A+      +       D  G+  S  + + +  ST EV+++++ A    I 
Sbjct: 20  LSALSETLGADLFVRDEDARAACLRDMTGNWPSGAQAVARPRSTAEVARLVQAAAAQGIA 79

Query: 71  VVVRGSGTGLVGAC-VPL-FGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEE 128
           +V +G  TGLVG C VP     ++L T  + +I  +D     V  E G +L E+ + V  
Sbjct: 80  IVPQGGNTGLVGGCAVPAETPALLLSTRRLRSIRAIDLHAPAVIAEAGCILAEVQEAVAA 139

Query: 129 NDLFYPPDPG-EKSATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIV 187
           +    P   G E SATI G +STNAGG+RA+++GV R+ V GL VVL +G +      + 
Sbjct: 140 HGFTIPLGLGSEGSATIGGLVSTNAGGIRALRHGVMRNQVLGLEVVLPDGRVWNGLRTLA 199

Query: 188 KNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKSK 247
           KN+ GY LK L IG EGTL V+T A L+L+P  +   +L +  E+ + A  ++  +  + 
Sbjct: 200 KNNMGYDLKQLFIGGEGTLGVVTAAALRLVPASRQIETLWLAVEDPAAALALLGALRTAL 259

Query: 248 A-IPTAIEFMERQTILFAEDFL-GKKFPDSSSNAYILL--TFDGNTKEQVEAEYETVANL 303
             + T+ E ++R+ + +    + G + PDS ++ + +L       T   + A  E     
Sbjct: 260 GDLVTSFELIQRRGVEWGMAAVPGLRVPDSGAHGWFVLAEVATAATGLPLRAAVEAALAD 319

Query: 304 CLAEG-AKDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAEFIEFTH 362
              +G A D  + ++  ++  +W  R A +   KA+       DV VP  ++  F+  T 
Sbjct: 320 VFEQGLALDGMLAESEAQRRELWRIREAVVVG-KAAGKPSISVDVAVPLGQVPAFLVETE 378

Query: 363 DLAKEM--DVRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRMYAKALTFEGLVS 420
             A  +        FGH GDGN+H  V R       +         ++ A AL   G + 
Sbjct: 379 AAAAGLLPGCETLGFGHLGDGNIHFSVHRGANDTERFAGTAEAIAAKVEAIALRLGGTIC 438

Query: 421 GEHGIGYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKVCQM 466
            EHG+G   R  + +      L L+  +K+  DP N +NP  V ++
Sbjct: 439 AEHGVGRRMRAAVADALDAAELDLIRAVKRALDPHNRMNPGAVIEL 484


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: 439
Number of extensions: 19
Number of successful extensions: 4
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: 484
Length adjustment: 33
Effective length of query: 433
Effective length of database: 451
Effective search space:   195283
Effective search space used:   195283
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.

Links

Downloads

Related tools

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