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_01369 CCNA_01369 acyl-CoA dehydrogenase, short-chain specific

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



>FitnessBrowser__Caulo:CCNA_01369
          Length = 379

 Score =  358 bits (918), Expect = e-103
 Identities = 188/373 (50%), Positives = 248/373 (66%), Gaps = 5/373 (1%)

Query: 1   MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQ-GLLGLPFSE 59
           MDF+ +EEQ ++++SV   L+  YDFD+R+K      GW    W  FAE+ G+LG  FSE
Sbjct: 1   MDFNFTEEQSMVRDSVASFLQDKYDFDTRRKIVSSDAGWRADYWKAFAEELGILGASFSE 60

Query: 60  EDGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGSK 119
           E GG G GA++ MI+ME  G +LV+EPYL TVVIGGGF++ +G A   A+ + GI+ GS 
Sbjct: 61  ELGGLGGGAIDNMIIMEEFGKALVIEPYLGTVVIGGGFMKHSGYAGA-ASVIEGIVGGST 119

Query: 120 TFAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDR 179
           T AFA  E  +R+   D+ TTAKK G GWV++G K VV+    A  LIVTART G QRD 
Sbjct: 120 TIAFAYAEPQARYTWQDLKTTAKKDGSGWVLNGHKAVVVGAPFATHLIVTARTGGAQRDA 179

Query: 180 TGVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDD 239
            GVGVF++     G+  + YPT DG  A+++ F  V + A+A I   E+ L L+E V+D+
Sbjct: 180 GGVGVFIIDKSLPGVVTRDYPTVDGNRASEVYFENVSIPAEALIS--ESGLALVEQVMDE 237

Query: 240 ARTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMF 299
           A  A+ AEAVG++ +    T++Y K RKQFG  I +FQVLQHR  DMF+  EQ+ SM   
Sbjct: 238 AIAAVGAEAVGVLRKLHEGTLDYAKQRKQFGTAIANFQVLQHRMVDMFIEVEQSVSMTYM 297

Query: 300 ATMAAEFDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTMI 359
           AT+    + A ERA A++A KV+IG++ KFVGQ +IQ+HGG+GMT E  IGHYFKR TMI
Sbjct: 298 ATIKVG-ESAAERAKAVSAMKVRIGRACKFVGQSAIQIHGGMGMTDELAIGHYFKRATMI 356

Query: 360 EQTFGDTDHHLAR 372
           E  FG  DHHL R
Sbjct: 357 EGLFGSVDHHLKR 369


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: 442
Number of extensions: 20
Number of successful extensions: 5
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: 379
Length adjustment: 30
Effective length of query: 350
Effective length of database: 349
Effective search space:   122150
Effective search space used:   122150
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