GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcd in Rhizobium leguminosarum bv. trifolii WSM1325

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_012760746.1 RLEG_RS35160 isovaleryl-CoA dehydrogenase

Query= BRENDA::Q18AQ1
         (378 letters)



>NCBI__GCF_000023185.1:WP_012760746.1
          Length = 381

 Score =  302 bits (774), Expect = 9e-87
 Identities = 157/367 (42%), Positives = 234/367 (63%)

Query: 11  LKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTVGYIM 70
           ++E    FA + + PLA E+DE   FP +   +M   G+ GI   +E+GG G   + +++
Sbjct: 13  IRETTARFAADHIAPLAVEIDESNTFPRQLWPEMGALGLHGITVEEEFGGAGLGYLDHVV 72

Query: 71  AVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLTEPNAG 130
           A+EE+SR   + G+   AH++L    I ++ + EQK+++L  L SGE +G+  ++E  AG
Sbjct: 73  AMEEVSRASASVGLSYGAHSNLCVNQIRRWASPEQKRRYLPKLISGEHVGSLAMSEVGAG 132

Query: 131 TDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFIVEKGTP 190
           +D    +  A   GD Y+LNG+K +ITNA   D+ VV A TD + G KGISA I+EKG P
Sbjct: 133 SDVVSMRLRAEKKGDRYVLNGTKFWITNAPHADVLVVYAKTDPAAGPKGISALIIEKGLP 192

Query: 191 GFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIGIAAQAL 250
           GF    K  K+G+RGS T+EL+FEDC +P E L+G+EG+G KI MS LD  R  +A   L
Sbjct: 193 GFGVSKKLSKLGMRGSDTAELVFEDCAVPAEALMGREGEGVKILMSGLDYERAVLAGGPL 252

Query: 251 GLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAINKDLGKP 310
           G+ Q  LD  + YV++R QFG+ +  FQ  Q ++ADM V + +AR  VY  A   D G+ 
Sbjct: 253 GIMQACLDVVLPYVRDRKQFGKAIGDFQLMQGKIADMYVALNSARAYVYSVARACDAGRA 312

Query: 311 YGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGTSEVQRM 370
              +AA A LFA+E A++V+ +A+Q  GG GYT+++PVER +RDAK+ +I  GT+E++R 
Sbjct: 313 TRTDAAAAILFASENAVKVSLEAIQALGGAGYTKEWPVERFLRDAKLYDIGAGTNEIRRY 372

Query: 371 VISGKLL 377
           +I  +L+
Sbjct: 373 LIGRELI 379


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: 353
Number of extensions: 13
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: 381
Length adjustment: 30
Effective length of query: 348
Effective length of database: 351
Effective search space:   122148
Effective search space used:   122148
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 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