GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctD in Dechlorosoma suillum PS

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate Dsui_0378 Dsui_0378 FAD/FMN-dependent dehydrogenase

Query= BRENDA::H6LBS1
         (466 letters)



>FitnessBrowser__PS:Dsui_0378
          Length = 465

 Score =  229 bits (584), Expect = 1e-64
 Identities = 139/445 (31%), Positives = 228/445 (51%), Gaps = 18/445 (4%)

Query: 26  GTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIPVVVRGSGTGLVGACV 85
           G  +      DE       P+ ++   STEEV+ +++   E+ +PV+  G G+ + G  +
Sbjct: 27  GESVRLQHGRDESKHEPMLPDGVVFAESTEEVAAVVRLCREYRVPVIPYGVGSSVEGHVL 86

Query: 86  PLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEENDLFYPPDPGEKSATIA 145
            + GGI ++ + MN +L +  E+L VTV+ GV   +L+  ++   LF+P DPG   AT+ 
Sbjct: 87  AVHGGISIDLSGMNRVLSIHAEDLDVTVQAGVTRKQLNDELKGTGLFFPIDPGA-DATLG 145

Query: 146 GNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKNSSGYSLKDLVIGSEGT 205
           G  +T A G  AV+YG  R+ V  LTVV   G+I+  G +  K+S+GY L  L +GSEGT
Sbjct: 146 GMAATRASGTNAVRYGTMRENVLSLTVVTPEGKIVRTGSRARKSSAGYDLTRLFVGSEGT 205

Query: 206 LCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKSKAIPTAIEFMERQTILFAE 265
           L +IT+  +KL P+P+   + +  F ++  A   V + I+       +E ++  T+    
Sbjct: 206 LGIITELTVKLYPIPEAMSAAVCAFPSVDAAVDTVIQTIQLGVPVARVELLDALTLQAIN 265

Query: 266 DFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCLAEGAKDVYIVDTVERKDSVW 325
            +     P++ +  +     D   +EQ E   E    +    G +D       E +  +W
Sbjct: 266 RYSKTTLPEAPTLFFEFHGSDSGVQEQAELTQE----IAQGNGGQDFQWATRQEDRSRLW 321

Query: 326 SAR-GAFLEAIKAST-TEMDECDVVVPRNRIAEFIEFTHDLAKEMDVRIPSFGHAGDGNL 383
            AR  A+   ++          DV VP +R+AE I  T++   ++ + I  FGH GDGN 
Sbjct: 322 QARHDAYFACLQLKPGARCFPTDVCVPISRLAECIHATNEDIAQVSLPIALFGHVGDGNF 381

Query: 384 HIYVCRD-----ELCQADWEAKLAEAMDRMYAKALTFEGLVSGEHGIGYAKRKYLLNDFG 438
           H+ V  D     E+ + +W ++      R+  +A+  EG  +GEHGIG  K+ YLL + G
Sbjct: 382 HLVVLVDTDNPKEMAEGEWISQ------RVVERAIAMEGTCTGEHGIGLGKQHYLLQEHG 435

Query: 439 TEHLALMAGIKQTFDPKNLLNPKKV 463
            + +ALM  +K   DP NL+NP K+
Sbjct: 436 EDGVALMRTLKTALDPLNLMNPGKI 460


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: 465
Number of extensions: 14
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: 465
Length adjustment: 33
Effective length of query: 433
Effective length of database: 432
Effective search space:   187056
Effective search space used:   187056
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