GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctC in Burkholderia phytofirmans PsJN

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized)
to candidate BPHYT_RS20830 BPHYT_RS20830 electron transfer flavoprotein subunit beta

Query= BRENDA::H6LBB1
         (418 letters)



>FitnessBrowser__BFirm:BPHYT_RS20830
          Length = 310

 Score =  143 bits (361), Expect = 6e-39
 Identities = 103/325 (31%), Positives = 172/325 (52%), Gaps = 27/325 (8%)

Query: 76  VYVDHIEGQIHPVTFELIGKARELAAVIGHPVYALLMGTNITEKADELLKY-GVDKVFVY 134
           V  +H    I   T   +  A++    IG  ++ L+ G N    AD   K  GV KV + 
Sbjct: 5   VIAEHDNASIKAATLNTVAAAQK----IGGDIHVLVAGHNAQAAADAAAKIAGVSKVLLA 60

Query: 135 DKPELKHFVIE----PYANVLEDFIEKVKPSSILVGATNVGRSLAPRVAARYRTGLTADC 190
           D P+L+  + E       N+ +D+      + IL  AT  G+++ PR+AA+      +D 
Sbjct: 61  DAPQLEAGLAENVEATVLNIAKDY------THILAPATAYGKNITPRIAAKLDVAQISDI 114

Query: 191 TILEMKENTDLVQIRPAFGGNIMAQIVTENTRPQFCTVRYKVFTAPERVNEPWGDVEMMD 250
           T ++  +  +    RP + GN +A + + +   +  TVR   F A   V    G   +  
Sbjct: 115 TAVDSADTFE----RPIYAGNAIATVQSADPI-KVITVRTTGFDA---VAAEGGSATVEK 166

Query: 251 IEKA--KLVSAIEVMEVIKKEKGIDLSEAETIVAVGRGV-KCEKDLDMIHEFAEKIGATV 307
           IE A    +S+    EV K ++  +L+ A+ IV+ GRG+   E    ++   A+K+ A +
Sbjct: 167 IEAAADSGISSFVSREVTKLDRP-ELTSAKVIVSGGRGLGNGENYTKVLEPLADKLNAAL 225

Query: 308 ACTRPGIEAGWFDARLQIGLSGRTVKPKLIIALGISGAVQFAAGMQNSEYIIAINSDPKA 367
             +R  ++AG+     Q+G +G+ V P+L IA+GISGA+Q  AGM++S+ I+AIN D +A
Sbjct: 226 GASRAAVDAGFVPNDYQVGQTGKIVAPQLYIAVGISGAIQHLAGMKDSKVIVAINKDEEA 285

Query: 368 PIFNIAHCGMVGDLYEILPELLTMI 392
           PIF++A  G+VGDL++ +P+L T +
Sbjct: 286 PIFSVADYGLVGDLFDAVPDLTTSV 310


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: 281
Number of extensions: 13
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: 310
Length adjustment: 29
Effective length of query: 389
Effective length of database: 281
Effective search space:   109309
Effective search space used:   109309
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