GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Korea:Ga0059261_1691
          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.

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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