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_043918838.1 jaqu_RS10025 acyl-CoA dehydrogenase family protein

Query= BRENDA::Q18AQ1
         (378 letters)



>NCBI__GCF_000877395.1:WP_043918838.1
          Length = 379

 Score =  259 bits (662), Expect = 9e-74
 Identities = 145/357 (40%), Positives = 212/357 (59%), Gaps = 3/357 (0%)

Query: 22  EVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTVGYIMAVEELSRVCGT 81
           E+ P A   +     P +   K+A+ G+ G+   +E GG G   +   +  E LS  C +
Sbjct: 23  EIAPHARAWEAAGDIPRDLWPKLAELGLAGLYVSEEAGGTGLTRLDATLVFEALSMACPS 82

Query: 82  TGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLTEPNAGTDASGQQTTAV 141
               LS H       I  YG++E K + L    + E   ++ LTEP +G+DA+  +T A 
Sbjct: 83  VASFLSIHNMCARM-IDAYGSDELKDRMLPKALTCETWLSYCLTEPGSGSDAAALKTRAE 141

Query: 142 LDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFIVEKGTPGFSFGVKEKKM 201
              + + L G+K FI+     D Y+VMA + ++ G +GISAF+VE GT G SFG  E KM
Sbjct: 142 RTNEGWRLTGTKAFISGGGYSDAYIVMARSGEA-GPRGISAFVVEDGTDGLSFGGLEDKM 200

Query: 202 GIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIGIAAQALGLAQGALDETV 261
           G R   T ++  +D  +P  NLLG+EG GF+ AM+ LDGGR+ IAA +LG AQ ALD T+
Sbjct: 201 GWRSQPTRQVQLDDAPVPASNLLGEEGHGFRYAMAGLDGGRLNIAACSLGAAQQALDLTL 260

Query: 262 KYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAINKDLGKPYGVE-AAMAKL 320
            YV+ER  FG+ L+ FQNTQF+LA+ME+++Q+AR  + QAA + D G P   +  AMAK 
Sbjct: 261 AYVRERKAFGQSLADFQNTQFRLAEMEIELQSARTFLRQAAWHLDQGTPEATKFCAMAKK 320

Query: 321 FAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGTSEVQRMVISGKLL 377
              E    V    +QLHGGYGY  DY +E++ RD ++ +I EGT+E+ R++++  +L
Sbjct: 321 MVTEAGSRVVDGCLQLHGGYGYLADYGIEKLSRDLRVHQILEGTNEIMRLIVARNML 377


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: 333
Number of extensions: 12
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: 379
Length adjustment: 30
Effective length of query: 348
Effective length of database: 349
Effective search space:   121452
Effective search space used:   121452
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