GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Magnetospirillum magneticum AMB-1

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2); phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate WP_011383016.1 AMB_RS02965 phosphomannomutase/phosphoglucomutase

Query= BRENDA::M1T754
         (460 letters)



>NCBI__GCF_000009985.1:WP_011383016.1
          Length = 460

 Score =  523 bits (1347), Expect = e-153
 Identities = 262/457 (57%), Positives = 324/457 (70%), Gaps = 2/457 (0%)

Query: 1   MSHKFDPTTLREYDIRGIVGKTLNPADATAIGRGFGTLLRRAGGTRAAVGYDGRHSSPLL 60
           M+H F PT LREYDIRGI+G+TL  ADA AIGR FGT +RR GG    +G+DGR SSP +
Sbjct: 1   MTHIFHPTILREYDIRGIIGETLFAADAEAIGRAFGTRVRRNGGHVVCLGWDGRLSSPEM 60

Query: 61  EAALVQGLIASGIDVVRVGLGPTPMLYYAEAVLEVDGGIMITGSHNPPDYNGFKMVFQHR 120
             AL +GL+A+G  V RVG GPTPMLY+A  V + DGGIM+TGSHNPP++NGFKMV   R
Sbjct: 61  AEALTKGLMAAGCTVRRVGRGPTPMLYFAAKVRDADGGIMVTGSHNPPNHNGFKMVLAGR 120

Query: 121 PFFGEDILKIGTMAAEGDWEEGEGTVTNADIMDMYVDRLIAGYQG-GAFKVAWDAGNGAA 179
           PFFG DI  +GT+AA GD+  GEG      + + YV RL   Y G    +V WD GNGA 
Sbjct: 121 PFFGPDIQSLGTIAAAGDFASGEGKAVEDSVFEEYVSRLAQDYDGLRDLRVVWDCGNGAT 180

Query: 180 GPVIEKLVKFLPGEHHLLYTDVDGDFPNHHPDPTEEKNLVDLKALVAEKGLDFGIGFDGD 239
           G V+  LVK LPG H +L+ ++DG FPNHHPDPTE  NLV L+  V  +    GI FDGD
Sbjct: 181 GEVLHALVKRLPGTHTVLFGEIDGHFPNHHPDPTEPHNLVALQDKVLTESAHLGIAFDGD 240

Query: 240 GDRIGAIDGKGRVVWGDQLLGILAEPVLKAVPGGTIIADVKTSQALYDRVAELGGKPLMW 299
           GDRIG +D +GR+++GDQ+L ILAE +LK++PG TIIADVK S+  +D V  +GG  +M 
Sbjct: 241 GDRIGVVDAEGRILYGDQILVILAEDLLKSLPGATIIADVKASKVFFDEVRRMGGNAVMG 300

Query: 300 KTGHSLIKAKMKEVDSPLGGEMSGHIFFAWDYYGFDDAIYAAVRLMGAV-RHSGKSLTEL 358
           +TGHSLIK +M E  +PL GEMSGHIFFA  YYGFDDA+YAA+RL+G V R    ++ + 
Sbjct: 301 RTGHSLIKTQMAETGAPLAGEMSGHIFFADRYYGFDDALYAAIRLLGIVARWDHTTIGQR 360

Query: 359 KDAMPAMVNTPEMRFQVDESRKFAVIEEVLQRLEADGADINRTDGARVNTPDGWWLLRAS 418
           +D +P MVNTPE+RF   E RKFAV+ EV  RLEA+GA  +  DG RV+TPDGWWLLRAS
Sbjct: 361 RDRLPHMVNTPELRFDCPEERKFAVVAEVKARLEAEGASFSAIDGVRVDTPDGWWLLRAS 420

Query: 419 NTQDVLVARAEAKDEAGLERLLKQIDTQLELSHIARG 455
           NTQ VLVAR EA    GL+ L + +  QL  S ++ G
Sbjct: 421 NTQAVLVARCEAASSEGLKHLRQTLADQLAASGVSLG 457


Lambda     K      H
   0.318    0.139    0.417 

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: 676
Number of extensions: 34
Number of successful extensions: 3
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: 460
Length of database: 460
Length adjustment: 33
Effective length of query: 427
Effective length of database: 427
Effective search space:   182329
Effective search space used:   182329
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 17 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