GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpO in Dyella japonica UNC79MFTsu3.2

Align Alpha-glycerophosphate oxidase; EC 1.1.3.21; Exported protein 6; Glycerol-3-phosphate oxidase (uncharacterized)
to candidate N515DRAFT_3909 N515DRAFT_3909 homodimeric glycerol 3-phosphate dehydrogenase (quinone) (EC 1.1.5.3)

Query= curated2:P35596
         (608 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3909
          Length = 499

 Score =  176 bits (446), Expect = 2e-48
 Identities = 170/549 (30%), Positives = 256/549 (46%), Gaps = 92/549 (16%)

Query: 20  LDLLIIGGGITGAGVALQAAASGLETGLIEMQDFAEGTSSRSTKLVHGGLRYLKQFDVEV 79
           +D+L++GGGI G G+A  A   GL   L E  D A  TSS STKL+HGGLRYL+QF+  +
Sbjct: 5   VDVLVVGGGINGTGIARDAVGRGLSVWLCEQDDLASHTSSASTKLIHGGLRYLEQFEFAL 64

Query: 80  VSDTVSERAVVQQIAPHIPKSDPMLLPVYDEDGATFSLFRLKVAMDLYD-LLAGVSNTPA 138
           V   ++ER ++ ++APHI      +LP           + +++ + LYD L  G  + P 
Sbjct: 65  VGKALAEREILLRVAPHIIWPLRFVLP---HQSHLRPAWMIRLGLFLYDHLQRGRRSLPG 121

Query: 139 ANKV-LSKDQVLERQPNLKKEGLVGGGVYLDFRNNDARLVIENIKRANQDGALIANHVKA 197
           + +V LS+  V   QP L+ E  + G VY D    DARLV+ N   A Q GA +  H + 
Sbjct: 122 SRRVRLSRHAV--GQP-LRDEFPI-GFVYSDAWVQDARLVVLNAMDAVQRGARVMTHTRC 177

Query: 198 EGFLFDESGKITGVVARDLLTDQVFEIKARLVINTTGPWS-DKVRNLSNKGTQFSQMRPT 256
                  SG+   +        QV E+ AR ++N TGPW+ D +  ++ +G     +R  
Sbjct: 178 VS--ARRSGE-RWLARLQSSNGQVTEVAARALVNATGPWAVDFLDEVAAEGHDHG-LRLV 233

Query: 257 KGVHLVVDSSKIKVSQPVYFDTGLG------DGRMVFVLPRENK-TYFGTTDTDYTGDLE 309
           KG H+VV         P  +D          D R+VF +P E + T  GTTD +Y GD  
Sbjct: 234 KGSHIVV---------PRLYDHRYAYIFQQPDRRIVFAIPYEREFTLIGTTDVEYRGDPA 284

Query: 310 HPKVTQEDVDYLLGIVNNRFPESNITIDDIESSWAGLRPLIAGNSASDYNGGNNGTISDE 369
           HP++  ++  YL   V NR+ +  I   D+  S++G+RPL+  +S         G  S+ 
Sbjct: 285 HPRIDTQETAYLCDAV-NRYFKRGIVPADVVWSYSGVRPLLDDDS---------GKASEV 334

Query: 370 SFDNLIATVESYLSKEKTREDVESAVSKLESSTSEKHLDPSAVSRGSSLDRDDNGLLTLA 429
           + D L+              ++E A                   RG+        LL + 
Sbjct: 335 TRDYLL--------------ELEQA-------------------RGAP-------LLNVF 354

Query: 430 GGKITDYRKMAEGAMERVVDILKAEFDRSFKLINSKTYPVSGGEL-NPANVDSEIEAFAQ 488
           GGK+T +RK+AE A++R+  +L             K +P+ GG++ +P  +  ++ A   
Sbjct: 355 GGKLTTFRKLAEEAVDRLAPLL----GNREPAWTGKGHPLPGGDIQDPGRLAEQLRA--- 407

Query: 489 LGVSRGLDSKEAHYLANLYGSNAPKVFALAHSLEQAPGLSLADTLS--LHYAMRNELTLS 546
                 L    A  LA+ YGS + +V   A SL        AD  +  + Y  R E   S
Sbjct: 408 --TRPWLGEAMAWRLAHTYGSQSVRVLGDAASLTGLGEHFGADLYASEVDYLRRYEWAGS 465

Query: 547 PVDFLLRRT 555
             D L RRT
Sbjct: 466 AEDVLWRRT 474


Lambda     K      H
   0.314    0.133    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: 554
Number of extensions: 26
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: 608
Length of database: 499
Length adjustment: 36
Effective length of query: 572
Effective length of database: 463
Effective search space:   264836
Effective search space used:   264836
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