GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdB in Pseudomonas fluorescens FW300-N2E2

Align branched-chain-2-oxoacid decarboxylase (subunit 2/2) (EC 4.1.1.72) (characterized)
to candidate Pf6N2E2_666 Acetoin dehydrogenase E1 component beta-subunit (EC 1.2.4.-)

Query= BRENDA::Q9HIA4
         (319 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_666
          Length = 338

 Score =  275 bits (704), Expect = 9e-79
 Identities = 155/329 (47%), Positives = 206/329 (62%), Gaps = 17/329 (5%)

Query: 5   QALNSAMDLKMSEDDSVIILGEDVGRD----------GGVFRVTDGLQAKYGPQRVIDTP 54
           QA+N A+  +M  D SV I+GEDV             GGV  VT GL  ++ P RV+DTP
Sbjct: 9   QAINEALAQEMRRDSSVFIMGEDVAGGAGAPGENDAWGGVLGVTKGLYDQF-PGRVLDTP 67

Query: 55  LSELGIVGMAIGMAVNGLKPIPEIQFQDFIYTSMDQIINQMAKIRYRSGGDYTVPLVLRT 114
           LSE+G VG A+G A  G++P+ E+ F DF    +DQI+NQ AK RY  GG  + PLV+RT
Sbjct: 68  LSEIGYVGAAVGAATCGVRPVCELMFVDFAGCCLDQILNQAAKFRYMFGGKASTPLVIRT 127

Query: 115 PVGGGIKGGLYHSQSGEAYFAHTAGLTVVSPSNPYDAKGLLISAIESPDPVIFLEPKRLY 174
            VG G++    HSQ   + + H  GL VV PS+PYDAKGLLI AI   DPVIF E K LY
Sbjct: 128 MVGAGLRAAAQHSQMLTSLWTHIPGLKVVCPSSPYDAKGLLIQAIRDNDPVIFCEHKLLY 187

Query: 175 RAQKVEVPDEKYTIPLRKANVLKQGNDVTIVTYGSMVPTVMSVA---SKSKYDVEVIDLR 231
             Q  EVP+E YTIP  +AN L+ G DVT+V+YG  V T M  A   +    D EVIDLR
Sbjct: 188 SMQG-EVPEELYTIPFGEANFLRDGKDVTLVSYGRTVNTAMDAARSLAGRGIDCEVIDLR 246

Query: 232 TIAPMDRDTIISSVKKTGRVVIVHEAPRTLGVGAEISAMISERAIEYLYAPIVRVTGPDT 291
           T +P+D D+I+ SV+KTGR+V++ EA     +  +ISA+++++A   L API  VT P T
Sbjct: 247 TTSPLDEDSILESVEKTGRLVVIDEANPRCSMATDISALVAQKAFGALKAPIEMVTAPHT 306

Query: 292 PFPY--RLEEYYLPNEGRINAALDRVMSF 318
           P P+   LE+ Y+P+  +I  A+  V+ +
Sbjct: 307 PVPFSDSLEDLYIPDAAKIEQAVLNVIEW 335


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: 292
Number of extensions: 14
Number of successful extensions: 5
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: 338
Length adjustment: 28
Effective length of query: 291
Effective length of database: 310
Effective search space:    90210
Effective search space used:    90210
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: 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