GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Haloechinothrix alba DSM 45207

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_089299712.1 CHB84_RS01840 phosphomannomutase/phosphoglucomutase

Query= BRENDA::Q8PGN7
         (450 letters)



>NCBI__GCF_900188115.1:WP_089299712.1
          Length = 452

 Score =  303 bits (777), Expect = 6e-87
 Identities = 186/451 (41%), Positives = 258/451 (57%), Gaps = 16/451 (3%)

Query: 9   KAYDIRGRVPDELNEDLARRIGVALAAQL---DQGPVVLGHDVRLASPALQEALSAGLRA 65
           KAYDIRG V ++L+ DL  + G A A  +       V +GHD+R +SP L  A + G+ +
Sbjct: 9   KAYDIRGVVGEQLDADLVAQFGGAFARLVLAEGASAVAVGHDMRDSSPGLAGAFARGVTS 68

Query: 66  SGRDVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPISSDTGLF 125
            G DV+ IGL  T+++YF +  L   G  M TASHNP +YNG+KL R  A P+  ++GL 
Sbjct: 69  QGVDVVSIGLASTDQLYFASGSLNLPGA-MFTASHNPAEYNGIKLCRAGAAPVGQESGLA 127

Query: 126 AIRDTV---AADTAAPGEPTASEQSRTDKTAYLEHLLSYVDRSTLKPLKLVVNAGNGGAG 182
            IR+ V     +    G          D  A+L HL   VD S  +PL++VV+AGNG AG
Sbjct: 128 EIREVVEQGVPEFVGAGGTVGERDVLGDYAAHLRHL---VDLSGSRPLRIVVDAGNGMAG 184

Query: 183 LIVDLLAPHLPFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNGADFGIAWDGDF 242
             V  +   LP E V ++ E DG+FPN   NPL P N      AV++ GAD G+A+DGD 
Sbjct: 185 HTVPTVFDGLPIEIVPMYFELDGSFPNHEANPLDPANLVDLQHAVREAGADAGLAFDGDA 244

Query: 243 DRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQVEEAGGIPVLCK 302
           DRC+  D  G  +    +  L+A   LAK+PG  ++H+   +    E V E GGIPV  +
Sbjct: 245 DRCYVIDERGEPVPPSAITALVAVRALAKEPGAAIIHNLITSRAVPEIVAEHGGIPVRTR 304

Query: 303 SGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQSGRSLADLVEA 362
            GH+FIK+KM   +A++GGE SAH+YFR+F  AD+GM+  L +   +      L+ L   
Sbjct: 305 VGHSFIKQKMAETDAIFGGEHSAHYYFRDFWRADTGMLAALHVLAALGAHDGPLSTLT-G 363

Query: 363 RMQKFPCSGEINFKVADAKASVARVMEHYASL-SPELDYTDGISADF--GQWRFNLRSSN 419
           R Q++  SGEIN  V D  A    V E +A+     +D  DG++ +   G W FNLR+SN
Sbjct: 364 RYQRYVASGEINSTVDDQHARQRAVREAFAARDGVGIDDLDGLTVELAGGAW-FNLRASN 422

Query: 420 TEPLLRLNVETRGDAALLETRTQEISNLLRG 450
           TEPLLRLNVE   + A+ E  T E+  ++RG
Sbjct: 423 TEPLLRLNVEAENEVAMREL-TDEVLAIIRG 452


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: 532
Number of extensions: 28
Number of successful extensions: 5
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: 452
Length adjustment: 33
Effective length of query: 417
Effective length of database: 419
Effective search space:   174723
Effective search space used:   174723
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