GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimD in Acidovorax sp. GW101-3H11

Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate Ac3H11_1711 Acyl-CoA dehydrogenase, long-chain specific, mitochondrial precursor (EC 1.3.99.13)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_1711
          Length = 393

 Score =  404 bits (1039), Expect = e-117
 Identities = 211/400 (52%), Positives = 275/400 (68%), Gaps = 12/400 (3%)

Query: 1   MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60
           MDL F+ EE AFRDEVR +   N+P     K+      T+ +M  W +IL KKGW    W
Sbjct: 1   MDLAFTPEEQAFRDEVRAWVHANLPQDISHKVHNALRLTRADMQGWAKILGKKGWLGFGW 60

Query: 61  PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120
           PKE+GG GW++VQ ++F EE   A AP+ + FG  MV PVI  FG+ EQ+KRFLP IA+ 
Sbjct: 61  PKEFGGPGWTAVQKHLFEEECALAGAPRIIPFGPVMVAPVIMAFGNAEQQKRFLPGIASG 120

Query: 121 DDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAK 180
           + WW QG+SEPGSGSDLAS+KT+AE+ GDK+I+NGQKTWTTL QH DW+F L RT    K
Sbjct: 121 EVWWSQGYSEPGSGSDLASVKTRAERVGDKYIVNGQKTWTTLGQHGDWMFNLVRTSNEGK 180

Query: 181 KQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAKFL 240
            Q GISF+L+DMK+KG+TVRPI+ +DG  EVNEVFFD+VEVP ENL+G+ENKGW YAK L
Sbjct: 181 PQTGISFLLLDMKSKGVTVRPIKLLDGECEVNEVFFDNVEVPAENLIGEENKGWTYAKHL 240

Query: 241 LGNERTGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALELTQL 300
           L +ERT IA V  SK  + R+K++A       + V +D +FRD++A +E+++ ALE+  L
Sbjct: 241 LSHERTNIADVNRSKRELERLKRIAKT-----EGVWDDQRFRDQIALLEVDIVALEMLVL 295

Query: 301 RVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPY-----DVHGDDDS 355
           RV++ E K GK   + A  +LKIKGSEIQQ   EL+M   GPF+ P+     +     + 
Sbjct: 296 RVLSAE-KSGKNSLDIA-GLLKIKGSEIQQRYAELMMLAAGPFSLPFIEEAMEAGWQGNF 353

Query: 356 NETMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLG 395
              +   A +A  YFN RK +IYGGSNE+QRNI+ + VLG
Sbjct: 354 PGGVTANAPLASTYFNLRKTTIYGGSNEVQRNIVAQTVLG 393


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: 504
Number of extensions: 23
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: 396
Length of database: 393
Length adjustment: 31
Effective length of query: 365
Effective length of database: 362
Effective search space:   132130
Effective search space used:   132130
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