GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpO in Stenotrophomonas chelatiphaga DSM 21508

Align Alpha-glycerophosphate oxidase; EC 1.1.3.21; Exported protein 6; Glycerol-3-phosphate oxidase (uncharacterized)
to candidate WP_083491969.1 ABB28_RS07835 glycerol-3-phosphate dehydrogenase

Query= curated2:P35596
         (608 letters)



>NCBI__GCF_001431535.1:WP_083491969.1
          Length = 501

 Score =  148 bits (373), Expect = 6e-40
 Identities = 162/549 (29%), Positives = 232/549 (42%), Gaps = 94/549 (17%)

Query: 20  LDLLIIGGGITGAGVALQAAASGLETGLIEMQDFAEGTSSRSTKLVHGGLRYLKQFDVEV 79
           LD+L++GGGI G G+A  AA   L   L E  D A  TSS S+KLVHGGLRYL+     +
Sbjct: 2   LDVLVVGGGINGTGIARDAAGRVLTVALCEQHDLASHTSSASSKLVHGGLRYLEHGQFGM 61

Query: 80  VSDTVSERAVVQQIAPHIPKSDPMLLPVYDEDGATFSLFRLKVAMDLYDLLAGVS-NTPA 138
           V  ++ ERAV+ +IAPH+ +  P +LP    +      + + + + LYD L G S   P 
Sbjct: 62  VRKSLQERAVLMRIAPHLVQPLPFVLP---HEAHLRPAWLIHLGLWLYDHLGGRSPQLPR 118

Query: 139 ANKVLSKDQVLERQPNLKKEGLVGGGVYLDFRNNDARLVIENIKRANQDGALIANHVKAE 198
           +  +  +   L       +E L  G  Y D +  DARLV+ N   A + GA I      E
Sbjct: 119 SRSLRLRGHPLGAP---LREDLRRGFTYTDAQAPDARLVVVNAIDAAERGAHIWTRTVCE 175

Query: 199 GFLFDESGKITGVVARDLLTDQVFEIKARLVINTTGPWSDK-VRNLSNKGTQFSQMRPTK 257
                  G    V  RD    Q   ++ R+++N TG W+ + V N+S   T+   +R  +
Sbjct: 176 QAWRQADG--WSVDLRDPDGTQ-RSVRTRMLVNATGAWAPRFVENISL--TRGVALRLVQ 230

Query: 258 GVHLVVDS-----SKIKVSQPVYFDTGLGDGRMVFVLPRENK-TYFGTTDTDYTGDLEHP 311
           G H+VV +         + QP        DGR+VF LP E+  T  GTTD D+ GD    
Sbjct: 231 GSHIVVPALYAHDHAYLLQQP--------DGRIVFALPFEDHYTLIGTTDVDFEGDPGAV 282

Query: 312 KVTQEDVDYLLGIVNNRFPESNITIDDIESSWAGLRPLIAGNSASDYNGGNNGTISDESF 371
            V     DYL    N  F +   +  DI   ++G+R L+                     
Sbjct: 283 HVDDAQRDYLCAAANRSFRQQT-SPRDIVWEFSGVRALL--------------------- 320

Query: 372 DNLIATVESYLSKEKTREDVESAVSKLESSTSEKHLDPSAVSRGSSLDRDDNG--LLTLA 429
                            +D E+              + SAV+R   LD D  G  LL + 
Sbjct: 321 -----------------DDPEA--------------EASAVTRDYRLDLDAEGAPLLNVL 349

Query: 430 GGKITDYRKMAEGAMERVVDILKAEFDRSFKLINSKTYPVSGGELNPANVDSEIEAFAQL 489
           GGK+T YR++AE A    VD+L      +     +  +  +G +L  A   +  +  A L
Sbjct: 350 GGKLTTYRRLAEEA----VDLLAGHAGTA-----APAWTATGAQLPGAERGTPAQCAAWL 400

Query: 490 GVS-RGLDSKEAHYLANLYGSNAPKVFALAHSLEQAPGLSLAD--TLSLHYAMRNELTLS 546
                 L  K A   +  YG+ A  +   A SL        AD     + Y   +E    
Sbjct: 401 ATQWPWLPPKLAARWSRTYGARATLILGQADSLAALGTHFGADLYEAEVRYLCTHEWARQ 460

Query: 547 PVDFLLRRT 555
             D L RRT
Sbjct: 461 ADDVLWRRT 469


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: 593
Number of extensions: 33
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: 501
Length adjustment: 36
Effective length of query: 572
Effective length of database: 465
Effective search space:   265980
Effective search space used:   265980
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 24 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