GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Caulo:CCNA_01412 CCNA_01412 acyl-CoA
           dehydrogenase, short-chain specific
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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