GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimC in Caulobacter crescentus NA1000

Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate CCNA_01884 CCNA_01884 acyl-CoA dehydrogenase, short-chain specific

Query= metacyc::MONOMER-20677
         (380 letters)



>FitnessBrowser__Caulo:CCNA_01884
          Length = 382

 Score =  273 bits (697), Expect = 8e-78
 Identities = 158/375 (42%), Positives = 214/375 (57%), Gaps = 2/375 (0%)

Query: 1   MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLLGLPFSEE 60
           M+FDLSEEQ+LLK+S         DF + +   +    +  A W + A+ G L L   E+
Sbjct: 1   MNFDLSEEQQLLKDSARRYGADHGDFTAWRARVERGEAYDAASWRRMADLGWLMLNVPED 60

Query: 61  DGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGSKT 120
           DGG GAG  ETM+V EA+G  L+L P++ T VI    L  A + A +A  + G+ +G   
Sbjct: 61  DGGLGAGPTETMVVAEAVGRYLMLVPFVSTGVIAPTLLT-AATEALRAHLMAGLAEGKLV 119

Query: 121 FAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDRT 180
            + A  E N R+DL  ++T A+    G+ + G K   L+G AAD  IV ART      + 
Sbjct: 120 ISLADAEPNGRFDLNRIATRAEAVEGGFRLTGAKSHALDGGAADWFIVPARTTAADDSQD 179

Query: 181 GVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDDA 240
           GV +FLVPA+ +G+T       D  H A +   GV V A   IG       L+   VD  
Sbjct: 180 GVSLFLVPAEIEGLTVMRSRAMDNRHNASLKLDGVVVPAANLIGGLGEGFPLLRDAVDRG 239

Query: 241 RTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMFA 300
             A  AEAVG MD     T+EY+KTRKQFG  +G+FQ LQHRA DM +A E+ARSM   A
Sbjct: 240 VVARLAEAVGAMDAVREMTMEYLKTRKQFGQTLGAFQALQHRAVDMAIACEEARSMMYLA 299

Query: 301 TMAAEFDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTMIE 360
           T+A       ER   IAAAK ++G++  +VG+Q++QLHGG+G T E  + HY KRL MI+
Sbjct: 300 TLALS-GAPVERRKVIAAAKARVGQTSLYVGRQAVQLHGGVGFTEELAVAHYLKRLIMID 358

Query: 361 QTFGDTDHHLARVSA 375
             FG+ DHH A ++A
Sbjct: 359 MAFGNADHHRAELAA 373


Lambda     K      H
   0.318    0.135    0.388 

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: 401
Number of extensions: 19
Number of successful extensions: 3
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: 380
Length of database: 382
Length adjustment: 30
Effective length of query: 350
Effective length of database: 352
Effective search space:   123200
Effective search space used:   123200
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: 41 (21.7 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