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_RS13550 BPHYT_RS13550 acyl-CoA dehydrogenase

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



>lcl|FitnessBrowser__BFirm:BPHYT_RS13550 BPHYT_RS13550 acyl-CoA
           dehydrogenase
          Length = 402

 Score =  422 bits (1085), Expect = e-123
 Identities = 211/404 (52%), Positives = 279/404 (69%), Gaps = 10/404 (2%)

Query: 1   MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60
           MDLNF+ EE AFR +V+ F +D +P +   K+  GR  T+++M EW+ ILN +GW   HW
Sbjct: 1   MDLNFTPEEEAFRADVQAFLRDKLPQRLADKVHGGRRLTRDDMAEWHAILNAQGWLANHW 60

Query: 61  PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120
           PKEYGG GW+ VQ +IF  E   A AP+ + FGV+M+GPV+  +GSE QK+ +LPRI + 
Sbjct: 61  PKEYGGPGWNPVQKFIFENECALAGAPRVVPFGVNMLGPVLIKYGSEAQKRHWLPRILDG 120

Query: 121 DDWWCQGFSEPGSGSDLASLKTKA----EKKGDKWIINGQKTWTTLAQHADWIFCLCRTD 176
            DWWCQG+SEPG+GSDLAS+KT A    + +G+ +++NGQKTWTTL   A+ IFCL R+ 
Sbjct: 121 SDWWCQGYSEPGAGSDLASVKTTAVRGVDAQGEHYLVNGQKTWTTLGHFANMIFCLVRSA 180

Query: 177 PAAKKQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDY 236
              +KQEGISF+L+DMKT G+ VRPI T+DG HEVNEVFF DV VP+ENLVG+ENKGW  
Sbjct: 181 TDVRKQEGISFLLIDMKTPGVEVRPIITLDGEHEVNEVFFTDVRVPVENLVGEENKGWTC 240

Query: 237 AKFLLGNERTGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALE 296
           AK+LL  ERT IA VG S     R++++AA+    G+P+ EDP F  ++A VEI+L+ ++
Sbjct: 241 AKYLLTYERTNIAGVGFSVAAFNRLRKIAAKQRRNGRPLAEDPAFAARMARVEIDLENMK 300

Query: 297 LTQLRVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPYDVHGDDDSN 356
            T LRV+A     G G P   SS+LKI+G+EI+Q  + L    +G +A P+      D  
Sbjct: 301 TTNLRVIA--AVAGGGVPGAESSMLKIRGTEIRQEISSLTRRAMGAYAQPFIEEALHDGF 358

Query: 357 ETM----DWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396
           E      D  A  A  YFNNRK+SI+GGSNEIQ+NII K +LGL
Sbjct: 359 EGTPVGPDEAASAASLYFNNRKLSIFGGSNEIQKNIISKMILGL 402


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: 468
Number of extensions: 13
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 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