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_RS36645 RR42_RS36645 acyl-CoA dehydrogenase

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



>FitnessBrowser__Cup4G11:RR42_RS36645
          Length = 402

 Score =  441 bits (1133), Expect = e-128
 Identities = 214/404 (52%), Positives = 286/404 (70%), Gaps = 12/404 (2%)

Query: 1   MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60
           MDL FS  E AFR+EVR F + ++PA  R K++  +   K++ V W+RIL+ +GW    W
Sbjct: 1   MDLRFSAAEQAFREEVRSFVQASLPADIRDKVLAHQRVEKDDYVRWHRILHARGWGAPTW 60

Query: 61  PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120
           PKE+GGTGW+++Q  IF  E   A AP+ L FG++M+GPV+  + S+E K+RFLPRI  V
Sbjct: 61  PKEWGGTGWNALQRLIFEIEAFRAGAPRLLPFGLTMIGPVLMKYASQEHKERFLPRIPTV 120

Query: 121 DDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAK 180
           +D+WCQG+SEPGSGSDLASLKT+A ++GD++I+NGQKTWTT+A  ADWIFCL RTD  +K
Sbjct: 121 EDFWCQGYSEPGSGSDLASLKTRAVRRGDRYIVNGQKTWTTMAHFADWIFCLVRTDSESK 180

Query: 181 KQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAKFL 240
            QEGIS +L+DMKT G+TVRPI T+DGGH+VNEV+F+DVEVP  NL+G+EN+GW YAK+L
Sbjct: 181 PQEGISMLLIDMKTPGVTVRPIVTLDGGHDVNEVWFEDVEVPAGNLLGEENRGWTYAKYL 240

Query: 241 LGNERTGIARVGMSKERIRRIKQLAAQVESG-GKPVIEDPKFRDKLAAVEIELKALELTQ 299
           LG+ERTGIA +G     +R++K  A Q   G G+P+I+D + RDK+A +E+++ ALE+  
Sbjct: 241 LGHERTGIAGIGHCNRELRQLKHYATQATDGAGRPLIDDVRMRDKIARIEMDIMALEMLL 300

Query: 300 LRVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPY--------DVHG 351
           LRV   +   G   P P +S++KI+GSEIQQ    L MEV GP A PY        +   
Sbjct: 301 LRVATQDAGRG---PGPEASIVKIRGSEIQQDLAMLQMEVAGPNAWPYSPRWLEAGEAPP 357

Query: 352 DDDSNETMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLG 395
            D       W A  A  YF+ RK SIYGG+ E+Q+NII K +LG
Sbjct: 358 ADAPLHAPAWAAPAASTYFDMRKTSIYGGTTEVQKNIISKMILG 401


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: 471
Number of extensions: 18
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: 402
Length adjustment: 31
Effective length of query: 365
Effective length of database: 371
Effective search space:   135415
Effective search space used:   135415
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