GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcd in Jannaschia aquimarina GSW-M26

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 WP_043917997.1 jaqu_RS05745 acyl-CoA dehydrogenase

Query= BRENDA::Q18AQ1
         (378 letters)



>NCBI__GCF_000877395.1:WP_043917997.1
          Length = 402

 Score =  203 bits (516), Expect = 8e-57
 Identities = 124/371 (33%), Positives = 194/371 (52%), Gaps = 6/371 (1%)

Query: 2   DLNSKKYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGE 61
           D  S+  +ML++   +FAE E+ P  T    +E    E   +M  AG++G+  P+EYGG 
Sbjct: 27  DQLSEDERMLRDAARAFAEAELAPGVTRAARDEVVDPEVFRRMGAAGLLGVTIPEEYGGL 86

Query: 62  GGDTVGYIMAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGA 121
           G   V Y +   E+ RV      ++S  +SL  +PI+ YG+E QK ++L  LASGE +G 
Sbjct: 87  GAGYVTYGLVAREIERVDSGYRSMMSVQSSLVMYPIHAYGSEAQKARWLPQLASGEAIGC 146

Query: 122 FGLTEPNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGIS 181
           FGLTEP+AG+D  G +T A      Y + G+K +I+NA   D++VV A  D       I 
Sbjct: 147 FGLTEPDAGSDPGGMKTRAEKTATGYRITGTKTWISNAPIADVFVVWAKLDGV-----IR 201

Query: 182 AFIVEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGG 241
            F++E+GTPG S      K+ +R S T E++ +   +P+E LL    +G K     L+  
Sbjct: 202 GFLIERGTPGLSAPKIGGKLSLRASVTGEIVMDGVEVPEEALL-PGVEGLKGPFGCLNRA 260

Query: 242 RIGIAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQA 301
           R GI+   +G A+       +Y  +R QFGRPL++ Q  Q +LADM+  +        + 
Sbjct: 261 RYGISWGVMGAAEACWHAARQYGLDRKQFGRPLAQTQLYQKKLADMQTAIGLGLQGSLRL 320

Query: 302 AINKDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIY 361
               + G       +M K      A++V  +A  +HGG G + ++ V R M + +    Y
Sbjct: 321 GRMMEAGTASPELVSMMKRNNCGAALDVARQARDMHGGNGISEEFGVMRHMINLETVNTY 380

Query: 362 EGTSEVQRMVI 372
           EGT +V  +++
Sbjct: 381 EGTHDVHALIL 391


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: 374
Number of extensions: 18
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: 378
Length of database: 402
Length adjustment: 30
Effective length of query: 348
Effective length of database: 372
Effective search space:   129456
Effective search space used:   129456
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 24 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