GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcd in Sphingomonas koreensis DSMZ 15582

Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate Ga0059261_3793 Ga0059261_3793 Acyl-CoA dehydrogenases

Query= BRENDA::Q18AQ1
         (378 letters)



>FitnessBrowser__Korea:Ga0059261_3793
          Length = 381

 Score =  280 bits (716), Expect = 5e-80
 Identities = 149/378 (39%), Positives = 224/378 (59%)

Query: 1   MDLNSKKYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGG 60
           M L+ + +  L +    F    ++PL +E++  +  P   VE+M   G+ G+   +E+GG
Sbjct: 1   MALDPETFDALIDTVRRFVAQRLRPLESEVEAADAIPDTIVEEMKALGLFGLSIAEEFGG 60

Query: 61  EGGDTVGYIMAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLG 120
            G   +       E+ R           +  +GS  +   G  EQK  +L  +ASGE + 
Sbjct: 61  LGLTMLEECRVAIEMGRTTPAFRSTFGTNVGIGSQGLVMAGTSEQKAAWLPRIASGEIIT 120

Query: 121 AFGLTEPNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGI 180
           +F LTEP+ G+D+   +  AV DGD Y L+G+K FITNA    ++ VMA T    G +G+
Sbjct: 121 SFALTEPDVGSDSGAVKARAVRDGDVYRLSGTKRFITNADKASLFTVMARTGDEPGARGV 180

Query: 181 SAFIVEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDG 240
           SAF+V +  PG S G  EKKMG +G+  +++IF+D  +P  N LG+EG+GFKIAM  LD 
Sbjct: 181 SAFLVPRDLPGISIGEPEKKMGQKGAKVADVIFDDVPVPAANRLGEEGEGFKIAMRVLDR 240

Query: 241 GRIGIAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQ 300
           GR+ I+A ++G+A+  + + V Y  ER QFG+P+++ Q  Q  LAD + +  AAR LV +
Sbjct: 241 GRLHISAVSVGVAERLIADCVAYASERKQFGKPIAEHQLIQAMLADSKTECLAARALVLE 300

Query: 301 AAINKDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEI 360
            A  KD GK   +E+A AKLFA E    V  +AVQ+ GG GY  DY +ER+ RD ++  I
Sbjct: 301 TAAAKDAGKDVVMESAAAKLFATEMVGRVADRAVQILGGAGYIEDYGIERLYRDVRLFRI 360

Query: 361 YEGTSEVQRMVISGKLLK 378
           YEGTS++Q+++I+ + LK
Sbjct: 361 YEGTSQIQQLIIARETLK 378


Lambda     K      H
   0.315    0.133    0.373 

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: 335
Number of extensions: 16
Number of successful extensions: 1
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: 378
Length of database: 381
Length adjustment: 30
Effective length of query: 348
Effective length of database: 351
Effective search space:   122148
Effective search space used:   122148
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: 42 (22.0 bits)
S2: 50 (23.9 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