GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpO in Pseudomonas putida KT2440

Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate PP_1073 PP_1073 glycerol-3-phosphate dehydrogenase (aerobic)

Query= SwissProt::O86963
         (609 letters)



>FitnessBrowser__Putida:PP_1073
          Length = 514

 Score =  157 bits (398), Expect = 8e-43
 Identities = 154/552 (27%), Positives = 247/552 (44%), Gaps = 91/552 (16%)

Query: 13  QETAKTTYDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYL 72
           Q      YD+ +IGGGI G G+A   A  G+K  L E  D A+ TSS S+KL+HGG+RYL
Sbjct: 10  QPPTANCYDLAVIGGGINGVGIAADAAGRGLKVFLCEKDDLAQHTSSASSKLIHGGLRYL 69

Query: 73  KTFDVEVVADTVRERAIVQQIAPHIPKPDPMLLPIYDEPGATFSLFSVKVAMDLYDRLAN 132
           + ++  +V + + ER ++   APHI KP   +LP    P      + ++  + LYD L  
Sbjct: 70  EHYEFRLVREALAEREVLLAKAPHIVKPMRFVLP--HRPHLR-PAWMIRAGLFLYDHLG- 125

Query: 133 VTGSKYENYLLTKEEVLAREPQLQAENLVGGGV-YLDFRNNDARLVIENIKRAQADGAAM 191
                 +   L     L   P    +  +  G  Y D   +DARLV+ N   A+  GA +
Sbjct: 126 ------KRKRLGASRSLRFGPGYPLKPAITRGFEYADCAVDDARLVVLNAMAARELGAHI 179

Query: 192 ISKAKVVGILHDEQGIINGV-EVEDQLTNERFE-VHAKVVINTTGPWSDIVRQLDKNDEL 249
            ++ +    L  E+  + G+ +VE Q  +   + +HA+ ++N  GPW     + D   + 
Sbjct: 180 RTRTR---CLRAER--VEGLWQVELQHADGSLQTIHARALVNAAGPWVASFIKDDLKLDA 234

Query: 250 PPQMRPTKGVHLVVDREKLKVPQPTYFDTGKNDGRMVFVVPRENK-TYFGTTDTDYTGDF 308
           P  +R  +G H++V R  L   +  Y      D R+VF +P  ++ T  GTTD +Y+GD 
Sbjct: 235 PYGIRLIQGSHIIVPR--LYEGEHAYI-LQNEDQRIVFCIPYLDRFTLIGTTDREYSGDP 291

Query: 309 AHPTVTQEDVDYLLTIVNERFPHAQITLDDIEASWAGLRPLITNNGGSDYNGGGKGKLSD 368
           A   +T+++  YLL +VNE F H Q++  DI  +++G+RPL                 +D
Sbjct: 292 AAVAITEQETHYLLKVVNEHFNH-QLSQADILHTYSGVRPL----------------CND 334

Query: 369 ESFEQIVESVKEYLADERQRPVVEKAVKQAQERVEASKVDPSQVSRGSSLERSKD----G 424
           ES                                     +PS V+R  +L  S +     
Sbjct: 335 ES------------------------------------DNPSAVTRDYTLALSAEVGQAP 358

Query: 425 LLTLAGGKITDYRLMAEGAVKRINELLQESGASFELVDSTTYPVSGGELDAANVEEELAK 484
           LL++ GGK+T YR +AE A+  +     +  A +    + + P+ G E     V+  +  
Sbjct: 359 LLSVFGGKLTTYRKLAESAMAELKPFFTQMRAPW----TASAPLPGAE-GMTTVQALIDA 413

Query: 485 LADQAQTAGFNEAAATYLAHLYGSNLPQVLNYKTKFEGLDEKESTAL-----NYSLHEEM 539
           +  +      + A    L   YGS + ++L+     E L +     L     +Y L EE 
Sbjct: 414 VLARCGWLPVDLAKRWVLT--YGSRVWRLLDGVHGPEDLGQAIGAGLFTREVDYLLEEEW 471

Query: 540 VLTPVDYLLRRT 551
                D + RRT
Sbjct: 472 AEQTADIIWRRT 483


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: 535
Number of extensions: 25
Number of successful extensions: 5
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: 514
Length adjustment: 36
Effective length of query: 573
Effective length of database: 478
Effective search space:   273894
Effective search space used:   273894
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.

Links

Downloads

Related tools

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