GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PPDCbeta in Pseudomonas fluorescens FW300-N2C3

Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate AO356_24885 AO356_24885 pyruvate dehydrogenase

Query= uniprot:G1UHX5
         (328 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_24885
          Length = 338

 Score =  195 bits (496), Expect = 1e-54
 Identities = 123/333 (36%), Positives = 173/333 (51%), Gaps = 13/333 (3%)

Query: 3   EITMAKALNTALRDALRDDPRTILFGEDIG----------ALGGVFRITDGLAAEFGDER 52
           +I+  +A+N AL   +R D    + GED+           A GGV  +T GL  +F   R
Sbjct: 4   KISYQQAINEALAQEMRRDSSVFIMGEDVAGGAGAPGENDAWGGVLGVTKGLYDQFPG-R 62

Query: 53  CFDTPLAESAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLP 112
             DTPL+E   +G AVG A  G RPV E+ F  FA    +Q+++  AK R    G    P
Sbjct: 63  VLDTPLSEIGYVGAAVGAATCGVRPVCELMFVDFAGCCLDQILNQAAKFRYMFGGKASTP 122

Query: 113 LTIRIPYGGGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLE 172
           L IR   G G+     HS      +   PGL VV P++  DA  LL ++I   DPV+F E
Sbjct: 123 LVIRTMVGAGLRAAAQHSQMLTSLWTHIPGLKVVCPSSPYDAKGLLIQAIRDNDPVIFCE 182

Query: 173 PKRLYWRKEALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEV 232
            K LY  +  +   + T P G A   R G   TL++YG  V TA++AA + A  G D EV
Sbjct: 183 HKLLYSMQGEVPEELYTIPFGEANFLRDGKDVTLVSYGRMVNTAMDAARSLAGRGIDCEV 242

Query: 233 IDLRTLMPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVT 292
           IDLRT  P+D+ ++  SV +TGR VV+ EA+       +++A + ++ F  L+AP+  VT
Sbjct: 243 IDLRTTSPMDEDSILESVEKTGRLVVIDEANPRCSMATDVSALVAQKAFGALKAPIEMVT 302

Query: 293 GFDVPYP-PPLLERHYLPGVDRILDAVAS-LEW 323
               P P    LE  Y+P   +I  AV + +EW
Sbjct: 303 APHTPVPFSDALEDLYIPDAAKIEQAVLNVIEW 335


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: 264
Number of extensions: 13
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: 338
Length adjustment: 28
Effective length of query: 300
Effective length of database: 310
Effective search space:    93000
Effective search space used:    93000
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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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