GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bkdB in Pseudomonas fluorescens FW300-N1B4

Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate Pf1N1B4_4479 Branched-chain alpha-keto acid dehydrogenase, E1 component, beta subunit (EC 1.2.4.4)

Query= reanno::pseudo5_N2C3_1:AO356_22985
         (352 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4479 Branched-chain
           alpha-keto acid dehydrogenase, E1 component, beta
           subunit (EC 1.2.4.4)
          Length = 352

 Score =  705 bits (1820), Expect = 0.0
 Identities = 342/352 (97%), Positives = 348/352 (98%)

Query: 1   MNDHNNNIALDTAMTTTTMTMIQALRSAMDVMLERDDNVVVFGQDVGYFGGVFRCTEGLQ 60
           MNDHNN I L+TAMTTTTMTMIQALRSAMDVMLERDDNVVVFGQDVGYFGGVFRCTEGLQ
Sbjct: 1   MNDHNNKIELETAMTTTTMTMIQALRSAMDVMLERDDNVVVFGQDVGYFGGVFRCTEGLQ 60

Query: 61  NKYGTSRVFDAPISESGIVGVAVGMGAYGLRPVAEIQFADYVYPASDQIISEAARLRYRS 120
           NKYGTSRVFDAPISESGIVGVAVGMGAYGLRPVAEIQFADYVYPASDQIISEAARLRYRS
Sbjct: 61  NKYGTSRVFDAPISESGIVGVAVGMGAYGLRPVAEIQFADYVYPASDQIISEAARLRYRS 120

Query: 121 AGEFTAPMTLRMPCGGGIYGGQTHSQSIEAMFTQVCGLRTVMPSNPYDAKGLLIASIEND 180
           AGEFTAPMTLRMPCGGGIYGGQTHSQSIEAMFTQVCGLRTVMPSNPYDAKGLLIASIEND
Sbjct: 121 AGEFTAPMTLRMPCGGGIYGGQTHSQSIEAMFTQVCGLRTVMPSNPYDAKGLLIASIEND 180

Query: 181 DPVIFLEPKRLYNGPFDGHHDRPVTPWSKHPSAQVPDGYYTVPLDVAAITRPGKDVTILT 240
           DPVIFLEPKRLYNGPFDGHHDRPVTPWSKHP+AQVPDGYYTVPLDVAAI RPGKDVTILT
Sbjct: 181 DPVIFLEPKRLYNGPFDGHHDRPVTPWSKHPAAQVPDGYYTVPLDVAAIARPGKDVTILT 240

Query: 241 YGTTVYVSQVAAEETGIDAEVIDLRSLWPLDLETIVKSVKKTGRCVVVHEATRTCGFGAE 300
           YGTTVYVSQVAAEETGIDAEVIDLRSLWPLDL+TIVKSVKKTGRCV+VHEATRTCGFGAE
Sbjct: 241 YGTTVYVSQVAAEETGIDAEVIDLRSLWPLDLDTIVKSVKKTGRCVIVHEATRTCGFGAE 300

Query: 301 LVSLVQEHCFHHLEAPIERVTGWDTPYPHAQEWAYFPGPSRVGAALKRVMEV 352
           LV+LVQEHCFH+LEAPIERVTGWDTPYPHAQEWAYFPGPSRVGAAL RVMEV
Sbjct: 301 LVALVQEHCFHYLEAPIERVTGWDTPYPHAQEWAYFPGPSRVGAALHRVMEV 352


Lambda     K      H
   0.320    0.136    0.417 

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: 580
Number of extensions: 10
Number of successful extensions: 1
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: 352
Length of database: 352
Length adjustment: 29
Effective length of query: 323
Effective length of database: 323
Effective search space:   104329
Effective search space used:   104329
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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