GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimD in Caulobacter crescentus NA1000

Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate CCNA_02215 CCNA_02215 acyl-CoA dehydrogenase

Query= metacyc::MONOMER-20676
         (396 letters)



>FitnessBrowser__Caulo:CCNA_02215
          Length = 403

 Score =  358 bits (920), Expect = e-103
 Identities = 192/407 (47%), Positives = 262/407 (64%), Gaps = 15/407 (3%)

Query: 1   MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHN--TKEEMVEWYRILNKKGWAVT 58
           MDL FS E++AF+ EVR +         R+++ + ++    K   V+W + L ++GWA  
Sbjct: 1   MDLAFSAEDLAFQQEVRDWIATAYDDDLRRQMSQSKNGYLDKAGQVKWQKKLAERGWAAP 60

Query: 59  HWPKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIA 118
            WP E GG G++  Q YIFN E+  A  P     G+ MV PVI  FGS+ QK + LP I 
Sbjct: 61  DWPVELGGAGFTPSQRYIFNMEMSLAGVPTSSPMGLKMVAPVIMAFGSDAQKAQHLPPIL 120

Query: 119 NVDDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPA 178
           N D WWCQG+SEPGSGSDLASL+ +A + GD +++NG K WTT AQ ADW+FCL RT   
Sbjct: 121 NSDIWWCQGYSEPGSGSDLASLQMRAVRDGDDYVLNGSKIWTTHAQWADWMFCLVRTSTE 180

Query: 179 AKKQEGISFILVDMKTKGITVRPIQTIDG----GHEVNEVFFDDVEVPLENLVGQENKGW 234
            K QEGISF+L+ M T GI ++P+ T+DG      E+N+VFFD+V VP+ N +G+ENKGW
Sbjct: 181 GKPQEGISFLLLRMDTPGIQIKPLPTLDGPPDNEQEINQVFFDNVRVPVANRIGEENKGW 240

Query: 235 DYAKFLLGNERTGIARVGMSKERIRRIKQLAA--QVESGGKPVIEDPKFRDKLAAVEIEL 292
            YAK+LL  ER      G+    ++++K++AA  + + GG+ +I+DP FR K+A +EI++
Sbjct: 241 TYAKYLLEFERGNAYAPGL-MNMLKKVKRIAALERADDGGR-LIDDPDFRSKIANLEIQV 298

Query: 293 KALELTQLRVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPY--DVH 350
           +AL  ++LR+ +  G  GK    PASS+LK  GSE QQA TEL +E +G +A P+  D  
Sbjct: 299 EALNASELRIFSGRGA-GK-NIGPASSMLKCVGSEHQQAITELTLEAVGNYATPFVRDTW 356

Query: 351 GD-DDSNETMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396
              +D     D+    AP YFN RK SIY GSNEIQRNI+ K VLGL
Sbjct: 357 SPANDGRAGPDYAGPAAPAYFNYRKASIYAGSNEIQRNIMAKMVLGL 403


Lambda     K      H
   0.317    0.135    0.411 

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: 466
Number of extensions: 18
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: 396
Length of database: 403
Length adjustment: 31
Effective length of query: 365
Effective length of database: 372
Effective search space:   135780
Effective search space used:   135780
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 (21.6 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