GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acdH in Caulobacter crescentus NA1000

Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate CCNA_01412 CCNA_01412 acyl-CoA dehydrogenase, short-chain specific

Query= reanno::pseudo3_N2E3:AO353_25680
         (375 letters)



>lcl|FitnessBrowser__Caulo:CCNA_01412 CCNA_01412 acyl-CoA
           dehydrogenase, short-chain specific
          Length = 381

 Score =  305 bits (781), Expect = 1e-87
 Identities = 159/372 (42%), Positives = 242/372 (65%), Gaps = 3/372 (0%)

Query: 5   DEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGY 64
           ++Q+ I DAAR FA+ +L P +A+WD    FP + + + AELGF G+ V E  GG     
Sbjct: 9   EDQVAIQDAARAFAEGQLAPHSADWDENKHFPVDVLRQAAELGFAGIYVNEDVGGSGLSR 68

Query: 65  LAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFALT 124
           L  ++  E ++ GD   +  +++HN    + I +FG+DD ++R+L  L +  ++ ++ LT
Sbjct: 69  LDASIIFEALSYGDVPVAAYLTIHNMASWM-IDRFGSDDLRQRYLPRLTTMELIASYCLT 127

Query: 125 EPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIV 184
           EP +GSDA++++T A+L+GDHYVLNG K FI+ G  + + +V A T    G +G+SAF+V
Sbjct: 128 EPGSGSDAAAMRTTAKLDGDHYVLNGGKAFISGGGVSDIYVVMARTG-GEGAKGVSAFVV 186

Query: 185 PTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVGI 244
                G      E K+G +A  T Q+ F++ +VPVANR+G+EGEG++ A+  L+GGR+ I
Sbjct: 187 EKGMEGLSFGANERKMGWNAQPTAQVNFDNCRVPVANRIGQEGEGFRFAMMGLDGGRLNI 246

Query: 245 ASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALR 304
           AS S+G A+ A + A+ Y   R  FG+P+ + QA+ F+LADMAT++  AR MV  AA   
Sbjct: 247 ASCSLGGAQFALDTAKAYLETRNQFGRPLKDFQALQFKLADMATELEAARLMVRRAAHAL 306

Query: 305 DSGKPALVE-ASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGT 363
           DS  P   +  +MAK FA++   +V + ALQ  GGYGYL D+PLER+ RD+RV QI EGT
Sbjct: 307 DSKHPEATKLCAMAKRFATDAGFQVANDALQLHGGYGYLQDYPLERLVRDLRVHQILEGT 366

Query: 364 SDIQRMVISRNL 375
           ++I R++I+R +
Sbjct: 367 NEIMRVIIAREM 378


Lambda     K      H
   0.319    0.134    0.389 

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: 369
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: 375
Length of database: 381
Length adjustment: 30
Effective length of query: 345
Effective length of database: 351
Effective search space:   121095
Effective search space used:   121095
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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