GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctC in Sphingomonas koreensis DSMZ 15582

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized)
to candidate Ga0059261_2885 Ga0059261_2885 Electron transfer flavoprotein, alpha subunit

Query= BRENDA::H6LBB1
         (418 letters)



>FitnessBrowser__Korea:Ga0059261_2885
          Length = 309

 Score =  134 bits (336), Expect = 5e-36
 Identities = 99/319 (31%), Positives = 165/319 (51%), Gaps = 20/319 (6%)

Query: 74  ITVYVDHIEGQIHPVTFELIGKARELAAVIGHPVYALLMGTNITEKADELLKY-GVDKVF 132
           + V+V+H    +   T   +    +L  V+     AL+ G      AD   K  GV KV 
Sbjct: 3   VLVWVEHDNNSVKDATLAAVTAGTKLGDVV-----ALVAGQGAQGAADAAAKIVGVSKVL 57

Query: 133 VYDKPELKHFVIEPYANVLEDFIEKVKPSSILVGATNVGRSLAPRVAARYRTGLTADCTI 192
           + D     H + E  A ++ + +      + +  AT  G+++APRVAA       ++   
Sbjct: 58  LADDAAYGHGLAENVAPLVAELMAGY--DAFVAPATTTGKNIAPRVAALLDVMQISEVLS 115

Query: 193 LEMKENTDLVQIRPAFGGNIMAQIVTENTRPQFCTVRYKVFTAPERVNEPWGD--VEMMD 250
           +E  +       RP + GN +A + + + + +  TVR   F   E+     G   VE + 
Sbjct: 116 VESADTFT----RPIYAGNAIATVKSADAK-KVLTVRGTAF---EKAATEGGSASVEAVS 167

Query: 251 IEKAKLVSAIEVMEVIKKEKGIDLSEAETIVAVGRGV-KCEKDLDMIHEFAEKIGATVAC 309
            +    +S+    E+ K E+  +L+ A+ IV+ GR +   E+   +I   A+K+GA V  
Sbjct: 168 GKGDSGLSSFVGAEIAKSERP-ELTSAKVIVSGGRALGSSEQFHGLIDPLADKLGAAVGA 226

Query: 310 TRPGIEAGWFDARLQIGLSGRTVKPKLIIALGISGAVQFAAGMQNSEYIIAINSDPKAPI 369
           +R  ++AG+     Q+G +G+ V P++ +A+GISGA+Q  AGM++S+ IIAIN D  API
Sbjct: 227 SRAAVDAGYAPNDYQVGQTGKIVAPEVYVAIGISGAIQHLAGMKDSKTIIAINKDEDAPI 286

Query: 370 FNIAHCGMVGDLYEILPEL 388
           F +A  G+VGDL++I+PEL
Sbjct: 287 FQVADLGLVGDLFKIVPEL 305


Lambda     K      H
   0.319    0.137    0.395 

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: 299
Number of extensions: 8
Number of successful extensions: 2
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: 418
Length of database: 309
Length adjustment: 29
Effective length of query: 389
Effective length of database: 280
Effective search space:   108920
Effective search space used:   108920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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:

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