GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Sphingomonas koreensis DSMZ 15582

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2); phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate Ga0059261_2456 Ga0059261_2456 Phosphomannomutase

Query= BRENDA::M1T754
         (460 letters)



>FitnessBrowser__Korea:Ga0059261_2456
          Length = 460

 Score =  741 bits (1912), Expect = 0.0
 Identities = 360/460 (78%), Positives = 397/460 (86%)

Query: 1   MSHKFDPTTLREYDIRGIVGKTLNPADATAIGRGFGTLLRRAGGTRAAVGYDGRHSSPLL 60
           ++H+FDPT+LREYDIRGIVGKTL P DA AIGRGF TLLRRAGG R AVG DGR SSP L
Sbjct: 1   VTHRFDPTSLREYDIRGIVGKTLGPDDARAIGRGFATLLRRAGGHRVAVGRDGRVSSPEL 60

Query: 61  EAALVQGLIASGIDVVRVGLGPTPMLYYAEAVLEVDGGIMITGSHNPPDYNGFKMVFQHR 120
           EAALV+GL ASG DVVRVG+GPTPMLYYAEA+LEVDGGI ITGSHNP DYNGFKMVFQHR
Sbjct: 61  EAALVEGLTASGCDVVRVGMGPTPMLYYAEAILEVDGGIQITGSHNPGDYNGFKMVFQHR 120

Query: 121 PFFGEDILKIGTMAAEGDWEEGEGTVTNADIMDMYVDRLIAGYQGGAFKVAWDAGNGAAG 180
           PFFG+DI +IG +A  GDW+EGEGTV++ADI+D YV RL AGY GG F++ WD GNGAAG
Sbjct: 121 PFFGQDIQEIGKLAEAGDWDEGEGTVSDADILDDYVGRLFAGYAGGTFRIGWDTGNGAAG 180

Query: 181 PVIEKLVKFLPGEHHLLYTDVDGDFPNHHPDPTEEKNLVDLKALVAEKGLDFGIGFDGDG 240
           PVIEKLV+ LPGEHH L+TDVDG+FPNHHPDPTEEKNL DL+ LVAEK LDFG+ FDGDG
Sbjct: 181 PVIEKLVQLLPGEHHTLFTDVDGNFPNHHPDPTEEKNLADLRRLVAEKNLDFGLAFDGDG 240

Query: 241 DRIGAIDGKGRVVWGDQLLGILAEPVLKAVPGGTIIADVKTSQALYDRVAELGGKPLMWK 300
           DRIGAIDG+GRV+WGDQLL ILAEPVLK  PG TIIADVK SQ L+DRVAELGG+PLMWK
Sbjct: 241 DRIGAIDGEGRVIWGDQLLSILAEPVLKKAPGATIIADVKASQMLFDRVAELGGQPLMWK 300

Query: 301 TGHSLIKAKMKEVDSPLGGEMSGHIFFAWDYYGFDDAIYAAVRLMGAVRHSGKSLTELKD 360
           TGHSL+K KMKE  SPL GEMSGHIFFA DYYGFDDA YAAV+L+ AV   G SLTE++ 
Sbjct: 301 TGHSLVKTKMKETHSPLAGEMSGHIFFAQDYYGFDDAQYAAVQLINAVHLIGTSLTEIRG 360

Query: 361 AMPAMVNTPEMRFQVDESRKFAVIEEVLQRLEADGADINRTDGARVNTPDGWWLLRASNT 420
            MPA VNTPEMRFQVDESRKFAVI+EVL RL+A GAD+N TDGARVNTPDGWWLLRASNT
Sbjct: 361 NMPAFVNTPEMRFQVDESRKFAVIDEVLDRLKATGADVNDTDGARVNTPDGWWLLRASNT 420

Query: 421 QDVLVARAEAKDEAGLERLLKQIDTQLELSHIARGEQAGH 460
           QDVLVARAEA+ +  L+RLL QID QLE S + RG QA H
Sbjct: 421 QDVLVARAEARSQEALDRLLAQIDAQLEASGLKRGPQAAH 460


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: 803
Number of extensions: 37
Number of successful extensions: 1
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