Alignments for a candidate for glpO in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpO in Herbaspirillum seropedicae SmR1

Align Alpha-glycerophosphate oxidase; EC 1.1.3.21; Exported protein 6; Glycerol-3-phosphate oxidase (uncharacterized)
to candidate HSERO_RS23645 HSERO_RS23645 glycerol-3-phosphate dehydrogenase

Query= curated2:P35596
         (608 letters)



>FitnessBrowser__HerbieS:HSERO_RS23645
          Length = 534

 Score =  169 bits (427), Expect = 4e-46
 Identities = 157/566 (27%), Positives = 245/566 (43%), Gaps = 77/566 (13%)

Query: 21  DLLIIGGGITGAGVALQAAASGLETGLIEMQDFAEGTSSRSTKLVHGGLRYLKQFDVEVV 80
           D+L++GGGI GAG+A  AA  GL   L E  D A+ TSS S+KL+HGGLRYL+ ++  +V
Sbjct: 16  DVLVVGGGINGAGIARDAAGRGLSVALCEQHDLAQHTSSSSSKLIHGGLRYLEHYEFGLV 75

Query: 81  SDTVSERAVVQQIAPHIPKSDPMLLPVYDEDGATFSLFRLKVAMDLYDLLAGVSNTPAAN 140
              + ER V+ + APHI      ++P    D      + +++ M LYD LA     P  +
Sbjct: 76  RKALIEREVLLRSAPHIMWPLRFVMP---HDQGQRPAWLIRLGMFLYDHLARRELLP-GS 131

Query: 141 KVLSKDQVLERQPNLKKEGLVGGGVYLDFRNNDARLVIENIKRANQDGALIANHVKAEGF 200
           + L   +     P   K     G VY D   +DARLV+ N   A + GA I    + E  
Sbjct: 132 RALDLRRHASGAP--LKAQFTRGFVYSDGWVDDARLVVLNAMDAAEKGAHIMTRTRCESL 189

Query: 201 LFDESGKITGVVARDLLTDQVFEIKARLVINTTGPWSDKVRNLSNKGTQFSQMRPTKGVH 260
              ++G    V+ R+       +++AR V+N  GPW  +    +        +R  KG H
Sbjct: 190 TRQDNG-WQAVLRRE--DGHAMQVRARCVVNAAGPWVAQFLGGAAHVHSSKSVRLVKGSH 246

Query: 261 LVVDSSKIKVSQPVYFDTGLGDGRMVFVLPRENK-TYFGTTDTDYTGDLEHPKVTQEDVD 319
           +VV   ++      Y      DGR+VF +P E   T  GTTD +Y G +E   ++ ++  
Sbjct: 247 IVV--PRLFEHDHAYIFQN-PDGRIVFAIPYEQDFTLIGTTDIEYQGRVEDVAISADETA 303

Query: 320 YLLGIVNNRFPESNITIDDIESSWAGLRPLIAGNSASDYNGGNNGTISDESFDNLIATVE 379
           YL  +  NR+ E  IT DD+  S++G+RPL+   +A                        
Sbjct: 304 YLCQLA-NRYFEKPITPDDVVWSYSGVRPLLEDAAA------------------------ 338

Query: 380 SYLSKEKTREDVESAVSKLESSTSEKHLDPSAVSRGSSLDRDDNG--LLTLAGGKITDYR 437
                                       D SAV+R   LD +  G  LL++ GGKIT +R
Sbjct: 339 ----------------------------DASAVTRDYQLDLNLQGAPLLSIFGGKITTFR 370

Query: 438 KMAEGAMERVVDIL---KAEFDRSFKLINSKTYPVSGGELNPANVDSEIEAFAQLGVSRG 494
           K+AE A++ +  +L   +  +     L     Y       +    D  ++   Q      
Sbjct: 371 KLAEEAVDMIAPVLGNQRGAWTEHGCLPGGDLYGAQPSNRSVRQFDQYVQGLQQ--QYPW 428

Query: 495 LDSKEAHYLANLYGSNAPKVFALAHSLEQAPGLSLADTL---SLHYAMRNELTLSPVDFL 551
           L +      A  YGS    +     ++E+  G  + D L    + Y +R+E   +  D L
Sbjct: 429 LPAALLQRYARAYGSRTHTLLEGRQNVEEM-GEEILDGLYAAEVDYLLRHEWASNAADIL 487

Query: 552 LRRTNHMLFMRDSLDSIVEPILDEMG 577
            RR+   L      +++++  L   G
Sbjct: 488 WRRSKLGLHFPKGSEAVLDAWLAARG 513


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: 627
Number of extensions: 39
Number of successful extensions: 6
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: 534
Length adjustment: 36
Effective length of query: 572
Effective length of database: 498
Effective search space:   284856
Effective search space used:   284856
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources