GapMind for catabolism of small carbon sources

 

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

Align branched-chain-2-oxoacid decarboxylase (subunit 2/2) (EC 4.1.1.72) (characterized)
to candidate Pf1N1B4_1019 Branched-chain alpha-keto acid dehydrogenase, E1 component, beta subunit (EC 1.2.4.4)

Query= BRENDA::Q9HIA4
         (319 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1019 Branched-chain
           alpha-keto acid dehydrogenase, E1 component, beta
           subunit (EC 1.2.4.4)
          Length = 329

 Score =  297 bits (761), Expect = 2e-85
 Identities = 156/320 (48%), Positives = 220/320 (68%), Gaps = 4/320 (1%)

Query: 1   MNMVQALNSAMDLKMSEDDSVIILGEDVGRDGGVFRVTDGLQAKYGPQRVIDTPLSELGI 60
           + +++A+N A+   MSED++VI+LGEDVG +GGVFR T GL+  +G +RVID+PL+E  +
Sbjct: 6   VTLLEAVNLALHRAMSEDENVIVLGEDVGVNGGVFRATLGLRDTFGFKRVIDSPLAETML 65

Query: 61  VGMAIGMAVNGLKPIPEIQFQDFIYTSMDQIINQMAKIRYRSGGDYTVPLVLRTPVGGGI 120
            G+ +GMA  GLKP+ EIQF  FIY +M+ +++  +++R R+ G  T P+V+R+P+G GI
Sbjct: 66  GGLVVGMAAQGLKPVVEIQFMGFIYATMEHLVSHASRMRNRTRGRITCPMVMRSPMGAGI 125

Query: 121 KGGLYHSQSGEAYFAHTAGLTVVSPSNPYDAKGLLISAIESPDPVIFLEPKRLYRAQKVE 180
           +   +HS+S EA FAH  GL VV PS+P  A GLL++AI+ PDPVIFLEP RLYR     
Sbjct: 126 RAPEHHSESTEALFAHIPGLRVVIPSSPARAYGLLLAAIDDPDPVIFLEPTRLYRMNPQP 185

Query: 181 VPDEKYTIPLRKANVLKQGNDVTIVTYGSMVPTVMSVASK---SKYDVEVIDLRTIAPMD 237
           + D+   +PL     L++G+D+T++++G+ V   +  A+K        EVID+ +I P+D
Sbjct: 186 LLDDGKRLPLDSCFTLREGSDITLISWGASVMETLQAATKLAEQGVSAEVIDVASIKPLD 245

Query: 238 RDTIISSVKKTGRVVIVHEAPRTLGVGAEISAMISERAIEYLYAPIVRVTGPDTPFP-YR 296
            DT+ +SV+KTGR VIVHEAPR+ GVGAEI+A + ER    L API RVT PD P P YR
Sbjct: 246 LDTMEASVRKTGRCVIVHEAPRSCGVGAEIAASLYERVFLELQAPIQRVTAPDIPPPLYR 305

Query: 297 LEEYYLPNEGRINAALDRVM 316
           LE  Y+P    I  A + VM
Sbjct: 306 LESLYMPGIEDILHACNTVM 325


Lambda     K      H
   0.318    0.137    0.388 

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: 305
Number of extensions: 15
Number of successful extensions: 2
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: 319
Length of database: 329
Length adjustment: 28
Effective length of query: 291
Effective length of database: 301
Effective search space:    87591
Effective search space used:    87591
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 (21.7 bits)
S2: 48 (23.1 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