GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcd in Caulobacter crescentus NA1000

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 CCNA_01412 CCNA_01412 acyl-CoA dehydrogenase, short-chain specific

Query= BRENDA::Q18AQ1
         (378 letters)



>FitnessBrowser__Caulo:CCNA_01412
          Length = 381

 Score =  301 bits (770), Expect = 3e-86
 Identities = 156/363 (42%), Positives = 235/363 (64%), Gaps = 3/363 (0%)

Query: 17  SFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTVGYIMAVEELS 76
           +FAE ++ P + + DE + FP + + + A+ G  GI   ++ GG G   +   +  E LS
Sbjct: 20  AFAEGQLAPHSADWDENKHFPVDVLRQAAELGFAGIYVNEDVGGSGLSRLDASIIFEALS 79

Query: 77  RVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLTEPNAGTDASGQ 136
                    L+ H ++ SW I ++G+++ +Q++L  L + E + ++ LTEP +G+DA+  
Sbjct: 80  YGDVPVAAYLTIH-NMASWMIDRFGSDDLRQRYLPRLTTMELIASYCLTEPGSGSDAAAM 138

Query: 137 QTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFIVEKGTPGFSFGV 196
           +TTA LDGD Y+LNG K FI+     DIYVVMA T   +G KG+SAF+VEKG  G SFG 
Sbjct: 139 RTTAKLDGDHYVLNGGKAFISGGGVSDIYVVMARTG-GEGAKGVSAFVVEKGMEGLSFGA 197

Query: 197 KEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIGIAAQALGLAQGA 256
            E+KMG     T+++ F++CR+P  N +G+EG+GF+ AM  LDGGR+ IA+ +LG AQ A
Sbjct: 198 NERKMGWNAQPTAQVNFDNCRVPVANRIGQEGEGFRFAMMGLDGGRLNIASCSLGGAQFA 257

Query: 257 LDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAINKDLGKPYGVE-A 315
           LD    Y++ R QFGRPL  FQ  QF+LADM  +++AAR +V +AA   D   P   +  
Sbjct: 258 LDTAKAYLETRNQFGRPLKDFQALQFKLADMATELEAARLMVRRAAHALDSKHPEATKLC 317

Query: 316 AMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGTSEVQRMVISGK 375
           AMAK FA +   +V   A+QLHGGYGY +DYP+ER++RD ++ +I EGT+E+ R++I+ +
Sbjct: 318 AMAKRFATDAGFQVANDALQLHGGYGYLQDYPLERLVRDLRVHQILEGTNEIMRVIIARE 377

Query: 376 LLK 378
           + +
Sbjct: 378 MFR 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: 348
Number of extensions: 15
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: 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 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