GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pimD in Burkholderia phytofirmans PsJN

Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate BPHYT_RS06715 BPHYT_RS06715 acyl-CoA dehydrogenase

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



>lcl|FitnessBrowser__BFirm:BPHYT_RS06715 BPHYT_RS06715 acyl-CoA
           dehydrogenase
          Length = 398

 Score =  460 bits (1184), Expect = e-134
 Identities = 226/407 (55%), Positives = 300/407 (73%), Gaps = 20/407 (4%)

Query: 1   MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60
           MDL++S  + AFR ++R + + N+P +   K++  +   +E+   W+++L  +GW+V  W
Sbjct: 1   MDLDYSPADNAFRADIRAWLEANLPRELSDKVLNHKRLAREDYAGWHKLLGTRGWSVIAW 60

Query: 61  PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120
           PKEYGG GW + Q +I++EE     AP  L FGVSMV PV+  +G+E QK+ +LPRI + 
Sbjct: 61  PKEYGGPGWDATQRHIWDEECARIGAPSVLPFGVSMVAPVLMKYGNEAQKRHYLPRILDG 120

Query: 121 DDWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAK 180
            DWWCQG+SEPGSGSDLASL+T+AE+ GD +++NGQKTWTTL Q+AD +FCL RTD  AK
Sbjct: 121 TDWWCQGYSEPGSGSDLASLRTRAERVGDHYVVNGQKTWTTLGQYADMMFCLVRTDGGAK 180

Query: 181 KQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAKFL 240
           KQEGISF+L+DMKT GITVRPI T+D  HEVNEVFF+DV+VP++NLVG+EN+GW YAK+L
Sbjct: 181 KQEGISFLLIDMKTPGITVRPIITLDEDHEVNEVFFEDVKVPVDNLVGEENRGWTYAKYL 240

Query: 241 LGNERTGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALELTQL 300
           LG+ERTGIARVG SK  +  +K+LA   +  GKP+++DP F  K+A++EIEL ALE+T  
Sbjct: 241 LGHERTGIARVGQSKRELVFLKRLALNQKKNGKPLLQDPVFAAKVASLEIELMALEVTVQ 300

Query: 301 RVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPYDV----------- 349
           RVVA+E   G+G P P +S+LKIKG+E+QQA TEL+ E +GP AAP+DV           
Sbjct: 301 RVVANE-TGGRG-PGPEASMLKIKGTEVQQALTELMFEAVGPLAAPFDVPFLEGEREHSL 358

Query: 350 HGDDDSNETMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396
            GDDD+       A +A  YFN RK SIYGGSNEIQ+NII + +LGL
Sbjct: 359 AGDDDA-------APLAAYYFNFRKTSIYGGSNEIQKNIIAQMILGL 398


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: 501
Number of extensions: 15
Number of successful extensions: 3
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: 398
Length adjustment: 31
Effective length of query: 365
Effective length of database: 367
Effective search space:   133955
Effective search space used:   133955
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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