GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpO in Burkholderia phytofirmans PsJN

Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate BPHYT_RS16490 BPHYT_RS16490 glycerol-3-phosphate dehydrogenase

Query= SwissProt::O86963
         (609 letters)



>FitnessBrowser__BFirm:BPHYT_RS16490
          Length = 509

 Score =  167 bits (424), Expect = 8e-46
 Identities = 161/576 (27%), Positives = 248/576 (43%), Gaps = 99/576 (17%)

Query: 15  TAKTTYDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLKT 74
           T  + YD+L++GGGI GAG+A   A  G+  +L E  D A  TSS STKL+HGG+RYL+ 
Sbjct: 2   TQGSRYDLLVVGGGINGAGIARDAAGRGLSVLLCEQDDLAAHTSSASTKLIHGGLRYLEY 61

Query: 75  FDVEVVADTVRERAIVQQIAPHIPKPDPMLLPIYDEPGATFSLFSVKVAMDLYDRLANVT 134
            +  +V   ++ER  + + APHI  P   ++P   +       + ++  + LYD LA   
Sbjct: 62  REFGLVRKALQERETLLRAAPHIMWPLRFVMPHMPD---LRPAWLIRAGLFLYDHLAR-- 116

Query: 135 GSKYENYLLTKEEVLAREPQLQA---ENLVGGGVYLDFRNNDARLVIENIKRAQADGAAM 191
                  L     ++ R     A   +++  G VY D   NDARLV+ N   AQ  GA +
Sbjct: 117 ----RELLPGSRGIVMRNHPAGAPLVDSIKRGFVYSDGWVNDARLVVLNALDAQEHGAKI 172

Query: 192 ISKAKVVGILHDEQGIINGVEVEDQL---TNERFEVHAKVVINTTGPWSDIVRQLDKNDE 248
           +++ K++        +  G E   QL        +V A  + N  GPW   + Q      
Sbjct: 173 LTRTKLL------SAVRAGGEWRAQLKRADGTLLDVRAASIANAAGPWVGELLQGALGRA 226

Query: 249 LPPQMRPTKGVHLVVDREKLKVPQPTYFDTGKNDGRMVFVVPRENK-TYFGTTDTDYTGD 307
               +R  KG H +V R   +      F     D R++F +P E+  T  GTTD +Y GD
Sbjct: 227 ASHSVRLVKGSH-IVTRRLFEHDHAYIFQ--NPDKRIIFAIPYEHDYTLIGTTDLEYRGD 283

Query: 308 FAHPTVTQEDVDYLLTIVNERFPHAQITLDDIEASWAGLRPLITNNGGSDYNGGGKGKLS 367
            +   +  ++  YL   +N  F   +I+  D+  +++G+RPL+   G             
Sbjct: 284 PSQVAINADETQYLCDSINRYFKQ-KISPADVRWTYSGVRPLLEEEGAD----------- 331

Query: 368 DESFEQIVESVKEYLADERQRPVVEKAVKQAQERVEASKVDPSQVSRGSSLE----RSKD 423
                                                   +PS V+R  SLE      + 
Sbjct: 332 ----------------------------------------NPSAVTRDYSLELDAPAGEA 351

Query: 424 GLLTLAGGKITDYRLMAEGAVKRINELLQESGASFELVDSTTYPVSGGELDAANVEEELA 483
            LL++ GGKIT +R +AE AV ++ + LQ   +S+    +   P+ GG++  AN E  L+
Sbjct: 352 PLLSVFGGKITTFRKLAEEAVDKLAQALQNGASSW----TAGAPLPGGDIPNANFERFLS 407

Query: 484 KLADQAQTAGFNEAAATYLAHLYGSNLPQVLNY--------KTKFEGLDEKESTALNYSL 535
           +   + Q A      A  LA  YG+ + QVL          +    GL E E   L Y  
Sbjct: 408 EF--KQQHAWLPADLAHRLARAYGTRVKQVLGNARSVADLGRAFAPGLYEAE---LTYLR 462

Query: 536 HEEMVLTPVDYLLRRTNHILFMR-DTLDDVKAGVVA 570
             E   +  D L RR+   L +   TLD +   + A
Sbjct: 463 DTEWARSAQDVLWRRSKLGLHVEPGTLDSITRDIDA 498


Lambda     K      H
   0.314    0.132    0.368 

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: 548
Number of extensions: 31
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 609
Length of database: 509
Length adjustment: 36
Effective length of query: 573
Effective length of database: 473
Effective search space:   271029
Effective search space used:   271029
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (25.0 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