GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Psychromonas ossibalaenae JAMM 0738

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_019614545.1 G327_RS26830 phosphomannomutase/phosphoglucomutase

Query= BRENDA::Q8PGN7
         (450 letters)



>NCBI__GCF_000381745.1:WP_019614545.1
          Length = 454

 Score =  491 bits (1264), Expect = e-143
 Identities = 241/445 (54%), Positives = 310/445 (69%), Gaps = 5/445 (1%)

Query: 5   LPAFKAYDIRGRVPDELNEDLARRIGVALAAQLDQGPVVLGHDVRLASPALQEALSAGLR 64
           L  FKAYDIRG + + LNED+  RIG A    L    V +G D+R  S   ++AL+ GL 
Sbjct: 4   LTCFKAYDIRGEIGENLNEDIVYRIGRAYCEWLKPKTVAVGGDIRKTSELFKQALAKGLM 63

Query: 65  ASGRDVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPISSDTGL 124
             G DVIDIG+ GTEE+Y+ T  L   GG+ VTASHNP+++NGMKLVRE A+PIS DTGL
Sbjct: 64  DGGCDVIDIGMVGTEEIYYATRSLNLDGGIEVTASHNPINFNGMKLVREDAKPISGDTGL 123

Query: 125 FAIRDTVAADTAAPGEPTASEQSRTDKTAYLEHLLSYVDRSTLKPLKLVVNAGNGGAGLI 184
            AI+     +  AP E     +  +++ AY+ HLLSY++   LKPLK+VVNAGNG AG  
Sbjct: 124 NAIKALAEENNFAPVENKGQYKLLSNRDAYVSHLLSYINAEQLKPLKIVVNAGNGAAGPT 183

Query: 185 VDLLAPH-----LPFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNGADFGIAWD 239
           +D +        +  EF++V HEPD +FPNGIPNP+L ENR  T KA+  +GAD GIAWD
Sbjct: 184 IDAIEERFKQTGVAVEFIKVNHEPDSSFPNGIPNPMLLENRTDTQKAILSHGADLGIAWD 243

Query: 240 GDFDRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQVEEAGGIPV 299
           GDFDRCFFFD    FIEGYY+VGLLA   L +  G K++HDPRLTWNT + V    G  +
Sbjct: 244 GDFDRCFFFDENAAFIEGYYIVGLLANTFLLQHAGEKIIHDPRLTWNTQDLVASLTGTAI 303

Query: 300 LCKSGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQSGRSLADL 359
             K+GHAFIKE+MR ENAVYGGEMSAHHYFR+F Y DSGMIPWLL+ EL+S+    L+ L
Sbjct: 304 ESKTGHAFIKERMRKENAVYGGEMSAHHYFRDFGYCDSGMIPWLLVIELISKKNEVLSKL 363

Query: 360 VEARMQKFPCSGEINFKVADAKASVARVMEHYASLSPELDYTDGISADFGQWRFNLRSSN 419
           VE R++ +P SGEIN  V+D + ++A + + Y + +  + + DG+S +F  WRFNLRSSN
Sbjct: 364 VEQRVELYPISGEINTLVSDPEKTIAAISDAYQAAALNVTHIDGLSMEFTDWRFNLRSSN 423

Query: 420 TEPLLRLNVETRGDAALLETRTQEI 444
           TE ++RLNVE+RG  AL+E +TQE+
Sbjct: 424 TEAVIRLNVESRGSQALVEQKTQEL 448


Lambda     K      H
   0.319    0.136    0.404 

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: 555
Number of extensions: 20
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 450
Length of database: 454
Length adjustment: 33
Effective length of query: 417
Effective length of database: 421
Effective search space:   175557
Effective search space used:   175557
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 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