GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PPDCbeta in Pseudomonas fluorescens FW300-N2E2

Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate Pf6N2E2_480 Branched-chain alpha-keto acid dehydrogenase, E1 component, beta subunit (EC 1.2.4.4)

Query= uniprot:G1UHX5
         (328 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_480 Branched-chain
           alpha-keto acid dehydrogenase, E1 component, beta
           subunit (EC 1.2.4.4)
          Length = 352

 Score =  270 bits (691), Expect = 3e-77
 Identities = 152/328 (46%), Positives = 194/328 (59%), Gaps = 21/328 (6%)

Query: 4   ITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAESAI 63
           +TM +AL +A+   L  D   ++FG+D+G  GGVFR T+GL  ++G  R FD P++ES I
Sbjct: 19  MTMIQALRSAMDVMLERDDNVVVFGQDVGYFGGVFRCTEGLQNKYGTSRVFDAPISESGI 78

Query: 64  LGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYGGGI 123
           +G AVGM  YG RPV E+QF  + YPA +Q++S  A+LR R+ G    P+T+R+P GGGI
Sbjct: 79  VGVAVGMGAYGLRPVAEIQFADYVYPASDQIISEAARLRYRSAGEFTAPMTLRMPCGGGI 138

Query: 124 GGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLY------ 177
            G + HS S E  +    GL  V P+   DA  LL  SI + DPV+FLEPKRLY      
Sbjct: 139 YGGQTHSQSIEAMFTQVCGLRTVMPSNPYDAKGLLIASIENDDPVIFLEPKRLYNGPFDG 198

Query: 178 --------WRKEALGLPVD---TGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEH 226
                   W K       D   T PL  A I R G   T++ YG   TT   +  AA E 
Sbjct: 199 HHDRPVTPWSKHPSAQVPDGYYTVPLDVAAITRPGKDVTVLTYG---TTVYVSQVAAEET 255

Query: 227 GWDLEVIDLRTLMPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEA 286
           G D EVIDLR+L PLD  T+  SV++TGR VVVHEA    G GAE+ A + E CF+HLEA
Sbjct: 256 GIDAEVIDLRSLWPLDLETIVKSVKKTGRCVVVHEATRTCGFGAELVALVQEHCFHHLEA 315

Query: 287 PVRRVTGFDVPYPPPLLERHYLPGVDRI 314
           P+ RVTG+D PY P   E  Y PG  R+
Sbjct: 316 PIERVTGWDTPY-PHAQEWAYFPGPSRV 342


Lambda     K      H
   0.322    0.138    0.418 

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: 349
Number of extensions: 17
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: 328
Length of database: 352
Length adjustment: 28
Effective length of query: 300
Effective length of database: 324
Effective search space:    97200
Effective search space used:    97200
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 (21.9 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, the preprint on GapMind for carbon sources, 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