GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etfA in Desulfoscipio geothermicus DSM 3669

Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_092483748.1 BM299_RS10480 electron transfer flavoprotein subunit alpha/FixB family protein

Query= BRENDA::D2RIQ3
         (340 letters)



>NCBI__GCF_900115975.1:WP_092483748.1
          Length = 325

 Score =  261 bits (668), Expect = 1e-74
 Identities = 142/324 (43%), Positives = 200/324 (61%), Gaps = 7/324 (2%)

Query: 13  KDLWVYVEHYKGEPVHVVYELLGECRKLADKCNQKLAAVLITDDAKDVPSKLIARGADLV 72
           K +WV+ E   G+   V +ELL E RK+AD+  ++L AVL+ +   D+ + L   GAD V
Sbjct: 3   KGIWVFAEQRDGQIKKVTFELLSEGRKIADQLGEELGAVLLGNGVADLAASLGEYGADKV 62

Query: 73  YVCQDPAFKYYSTDEYTNAFCEMIDEYQPSSVFIGATNDGRDLGPRIAARVNTGLCADCT 132
           YV    A + Y+TD YTN   +++ +Y PS + +G T  GRDL  ++A R+ TGL  DCT
Sbjct: 63  YVADSDALENYTTDGYTNVIADLVKQYAPSVLLMGCTVTGRDLAAQVAQRLETGLMTDCT 122

Query: 133 ILDAEEDGLIEWTRPAAGGNIMATILCKEHRPQMGTVRPKTFKAMEPDASRTGEVINYTL 192
            ++   DG + +TRP   G  +    C E RP M T+RP TF       ++  E+IN T 
Sbjct: 123 GMEIA-DGQLVFTRPIYAGKAIVKAACPEARPVMATIRPNTFAVQA--GAKEAEIINVTP 179

Query: 193 KN-HVDDRVTCIRREEVVSEGEMAIDDAPFVCSGGRGMKAKENFSLLYDLAHALGGAVGG 251
              ++   +  I R+  VSE    + +A  + SGGRGMK  ENF LL +LA  LG AVG 
Sbjct: 180 NTGNIRQVIKDIVRQ--VSE-RPELTEADIIVSGGRGMKGPENFKLLEELADVLGAAVGA 236

Query: 252 SRAAVDEGFIEHPRQVGQSGKTVTPKIYFACGISGSVQHKAGMSKSDTIVCINKDPDAPM 311
           SRAAVD G+I    QVGQ+GKTV+P +Y ACGISG++QH AGMS +  IV INKD +A +
Sbjct: 237 SRAAVDAGWIPQSFQVGQTGKTVSPVLYIACGISGAIQHLAGMSSAKCIVAINKDEEANI 296

Query: 312 FEISKYGIVGDALKILPLLTAKIK 335
           F+++ YGIVGD  +++P+L  ++K
Sbjct: 297 FKVADYGIVGDLFEVVPILKEELK 320


Lambda     K      H
   0.318    0.136    0.406 

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: 313
Number of extensions: 16
Number of successful extensions: 3
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: 340
Length of database: 325
Length adjustment: 28
Effective length of query: 312
Effective length of database: 297
Effective search space:    92664
Effective search space used:    92664
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: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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