GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimD in Cupriavidus basilensis 4G11

Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate RR42_RS05595 RR42_RS05595 acyl-CoA dehydrogenase

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



>FitnessBrowser__Cup4G11:RR42_RS05595
          Length = 400

 Score =  461 bits (1187), Expect = e-134
 Identities = 232/402 (57%), Positives = 298/402 (74%), Gaps = 8/402 (1%)

Query: 1   MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60
           MDLN+S  + AFR EVR + + N+PA+   K++  R   ++++V W+++L  +GW+  HW
Sbjct: 1   MDLNYSASDDAFRAEVRGWLEANLPAEISSKILNHRRPNRDDLVRWHKLLAGRGWSAPHW 60

Query: 61  PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120
           P +YGGTGW++ Q +I++EE     AP  L FGV+MV PVI  +GSE QK  +LPRI + 
Sbjct: 61  PVQYGGTGWNATQRHIWDEENARVGAPGVLPFGVAMVAPVIMKYGSEAQKSYYLPRILDC 120

Query: 121 DDWWCQGFSEPGSGSDLASLKTKAE--KKGDKWIINGQKTWTTLAQHADWIFCLCRTDPA 178
            DWWCQG+SEPGSGSDLASLKT+AE    G  +I+NGQKTWTTL QHAD IFCL RTD  
Sbjct: 121 TDWWCQGYSEPGSGSDLASLKTRAELTSDGKHYIVNGQKTWTTLGQHADMIFCLVRTDFE 180

Query: 179 AKKQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAK 238
           AKKQEGISF+L+DMKT GITVRPI  +D  HEVNEVFFD+V+VP+EN VG+EN+GW YAK
Sbjct: 181 AKKQEGISFLLIDMKTPGITVRPIIMLDEEHEVNEVFFDNVQVPVENRVGEENRGWTYAK 240

Query: 239 FLLGNERTGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALELT 298
           +LLG+ERTGIARVG SK  +  +K++A Q +  G+P++EDP F  K+AA+EIEL ALELT
Sbjct: 241 YLLGHERTGIARVGNSKRELGFLKRVAKQQQKNGRPLLEDPLFGAKVAALEIELMALELT 300

Query: 299 QLRVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPYDVHGDDDSNE- 357
            LRVV+ E   GKG P P +S+LKIKG+EIQQ  TEL++E +GP+A P+D    +  +E 
Sbjct: 301 VLRVVSSESA-GKG-PGPEASMLKIKGTEIQQMLTELMVEAVGPYAQPFDTAYLECEHEH 358

Query: 358 ---TMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396
                D  A +A  YFN RK SIYGGSNEIQ+NII + +LGL
Sbjct: 359 AVTGYDDAAPLAAYYFNYRKTSIYGGSNEIQKNIISQMILGL 400


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: 463
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: 396
Length of database: 400
Length adjustment: 31
Effective length of query: 365
Effective length of database: 369
Effective search space:   134685
Effective search space used:   134685
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