GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcd in Cupriavidus basilensis 4G11

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 RR42_RS28565 RR42_RS28565 acyl-CoA dehydrogenase

Query= BRENDA::Q18AQ1
         (378 letters)



>FitnessBrowser__Cup4G11:RR42_RS28565
          Length = 377

 Score =  341 bits (875), Expect = 2e-98
 Identities = 171/372 (45%), Positives = 247/372 (66%)

Query: 5   SKKYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGD 64
           S++  M+++   +FA   + P A E D   + P E V +M   G++G+  P+E+GG   D
Sbjct: 6   SEQQTMIRDTARTFASERLAPCAAEWDRAGQLPAEVVAEMGALGLLGMIVPEEWGGTYTD 65

Query: 65  TVGYIMAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGL 124
            + Y +A+EE++  C     ++S H S+G  PI  YG + QK+++L  LASGE +GAF L
Sbjct: 66  YIAYALAIEEIAAGCAACATLMSVHNSVGCGPILHYGTQAQKERYLPRLASGEIIGAFCL 125

Query: 125 TEPNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFI 184
           TEP AG++A   +T A    + ++L+GSK F+TN     + +V A T+ ++G +G+SAF+
Sbjct: 126 TEPQAGSEAHNLRTRARATDNGWVLSGSKQFVTNGQRAGVAIVFAATEPAQGKRGLSAFV 185

Query: 185 VEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIG 244
           V   TPGFS    E+KMGIR S T  +  +DC++P + LLG+ G+G +IA+S L+GGRIG
Sbjct: 186 VPTDTPGFSVHTPERKMGIRASDTCAITLDDCQVPHDALLGEPGEGLRIALSNLEGGRIG 245

Query: 245 IAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAIN 304
           IAAQALG+A+ A +   +Y  ERVQFGRPL +       LADM  ++ AAR LV++AA  
Sbjct: 246 IAAQALGIARSAFEAACRYAAERVQFGRPLREHAPIANMLADMATELNAARLLVHRAAHM 305

Query: 305 KDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGT 364
           +  G+P   EA+ AKL+A+E A  V +KA+Q+HGGYGY  DYPVER  RDA+IT+IYEGT
Sbjct: 306 RTAGQPCLSEASQAKLYASELAERVCSKALQIHGGYGYLEDYPVERHYRDARITQIYEGT 365

Query: 365 SEVQRMVISGKL 376
           SE+QRM+I+  L
Sbjct: 366 SEIQRMLIARTL 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: 315
Number of extensions: 8
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: 377
Length adjustment: 30
Effective length of query: 348
Effective length of database: 347
Effective search space:   120756
Effective search space used:   120756
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