GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Streptacidiphilus oryzae TH49

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_051939761.1 BS73_RS09785 phosphomannomutase/phosphoglucomutase

Query= BRENDA::Q8PGN7
         (450 letters)



>NCBI__GCF_000744815.1:WP_051939761.1
          Length = 465

 Score =  326 bits (836), Expect = 8e-94
 Identities = 196/449 (43%), Positives = 252/449 (56%), Gaps = 10/449 (2%)

Query: 9   KAYDIRGRVPDELNEDLARRIGVALAAQLDQGPVVLGHDVRLASPALQEALSAGLRASGR 68
           KAYDIRG VPD+ +E  A   G A       G +V GHD+R +SP L  A + G  A G 
Sbjct: 20  KAYDIRGVVPDDWDEATAELFGAAFVRVTGAGAIVTGHDMRPSSPGLAAAFARGATAQGA 79

Query: 69  DVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPISSDTGLFAIR 128
           DV +IGLC T+++YF +  L  AG  M TASHNP  YNG+KL R  A P+  DTGL AIR
Sbjct: 80  DVTEIGLCSTDQLYFASGSLGLAGA-MFTASHNPARYNGIKLCRAGAEPVGQDTGLAAIR 138

Query: 129 DTVAA--DTAAPGEPTASEQSRTDKTA----YLEHLLSYVDRSTLKPLKLVVNAGNGGAG 182
             V    D     EP A  + RT        Y  HL S VD   ++PLK+VV+AGNG  G
Sbjct: 139 ALVEEWLDAGRGPEPAAGPRGRTTSRETLADYAAHLRSLVDLGAIRPLKVVVDAGNGMGG 198

Query: 183 LIVDLLAPHLPFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNGADFGIAWDGDF 242
             V  +   LP   V ++ E DG FP+   NPL P N       V+  GAD G+A+DGD 
Sbjct: 199 HTVPTVLAGLPLTVVPMYFELDGTFPHHEANPLDPANIVDLRARVRAEGADLGLAFDGDA 258

Query: 243 DRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQVEEAGGIPVLCK 302
           DRCF  D  G  +    +  L+A   LA+ PG  V+H+   +    E V EAGGIPV  +
Sbjct: 259 DRCFVVDERGEPVSPSAVTALVAARELAEHPGAAVIHNLITSRTVPEVVREAGGIPVRTR 318

Query: 303 SGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQSGRSLADLVEA 362
            GH+FIK +M    AV+GGE SAH+YFR+F  AD+GM+  L +   + +  R L++L  A
Sbjct: 319 VGHSFIKAEMARAGAVFGGEHSAHYYFRDFWNADTGMLAALHVLAALGEQPRPLSELT-A 377

Query: 363 RMQKFPCSGEINFKVADAKASVARVMEHYASL-SPELDYTDGISADFGQWRFNLRSSNTE 421
           R +++  SGEIN  VAD    +A V   ++      LD  DG++     W FNLR SNTE
Sbjct: 378 RYERYAASGEINSTVADQAERIAAVRAAWSGRPGVTLDELDGLTVAGRDWWFNLRPSNTE 437

Query: 422 PLLRLNVETRGDAALLETRTQEISNLLRG 450
           PLLRLNVE R   A+   R  E+  L+RG
Sbjct: 438 PLLRLNVEARDRPAMAALR-DEVLALVRG 465


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: 585
Number of extensions: 32
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: 465
Length adjustment: 33
Effective length of query: 417
Effective length of database: 432
Effective search space:   180144
Effective search space used:   180144
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