GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcd in Psychrobacter cryohalolentis K5

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_011513566.1 PCRYO_RS06325 acyl-CoA dehydrogenase

Query= BRENDA::Q18AQ1
         (378 letters)



>NCBI__GCF_000013905.1:WP_011513566.1
          Length = 384

 Score =  291 bits (745), Expect = 2e-83
 Identities = 152/363 (41%), Positives = 230/363 (63%), Gaps = 2/363 (0%)

Query: 18  FAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTVGYIMAVEELSR 77
           F  N++ P+   + E +R P + + +M + G+ G+  P+EYGG G      +    EL R
Sbjct: 18  FVNNQLIPMEHWVAENDRLPDDIINQMRELGLFGLTIPEEYGGLGVTMEEEVTLAFELGR 77

Query: 78  VCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLTEPNAGTDASGQQ 137
                  ++  +  +GS  +   G E QKQK+L  LASGE +G+F LTEP++G+DA+  +
Sbjct: 78  TSPAFRSLIGTNNGIGSSGLVIDGTEAQKQKYLPRLASGEIIGSFCLTEPDSGSDAASLK 137

Query: 138 TTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTD-KSKGNKGISAFIVEKGTPGFSFGV 196
           TTA+ DGD YI+NG+K +ITNA    ++ VMA TD ++K + GISAFIVE  TPG + G 
Sbjct: 138 TTAIKDGDTYIINGTKRYITNAPEAGVFTVMARTDPQNKRSGGISAFIVESDTPGITLGK 197

Query: 197 KEKKMGIRGSATSELIFEDCRIPKENLLGK-EGQGFKIAMSTLDGGRIGIAAQALGLAQG 255
            +KKMG +G+ T ++IF++C +P + L+G  EG GFK AM  LD GR+ IAA + G A  
Sbjct: 198 IDKKMGQKGAHTCDVIFDNCIVPADALIGGVEGVGFKTAMKVLDKGRLHIAAASTGAATR 257

Query: 256 ALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAINKDLGKPYGVEA 315
            LD+ + Y  ER QFG+P++ FQ  Q  LAD + ++ AA+ +V  A+  +D GK    E+
Sbjct: 258 MLDDALHYAVERKQFGQPIANFQLIQAMLADSKAEIYAAKSMVLDASRLRDEGKDVVTES 317

Query: 316 AMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGTSEVQRMVISGK 375
           + AK+FA E    V  +AVQ+HGG GY  DY +ER  RD ++  +YEGT+++Q+++I+  
Sbjct: 318 SCAKMFATEMCGRVADRAVQIHGGAGYIADYGIERFYRDVRLYRLYEGTTQIQQIIIARN 377

Query: 376 LLK 378
           ++K
Sbjct: 378 MIK 380


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: 332
Number of extensions: 12
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: 378
Length of database: 384
Length adjustment: 30
Effective length of query: 348
Effective length of database: 354
Effective search space:   123192
Effective search space used:   123192
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