GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Escherichia coli BW25113

Align Phosphogluconate dehydratase; 6-phosphogluconate dehydratase; EC 4.2.1.12 (characterized)
to candidate 14407 b0269 CP4-6 prophage; predicted dehydratase (NCBI)

Query= SwissProt::P21909
         (607 letters)



>FitnessBrowser__Keio:14407
          Length = 655

 Score =  189 bits (480), Expect = 3e-52
 Identities = 168/500 (33%), Positives = 241/500 (48%), Gaps = 38/500 (7%)

Query: 80  LSAHEPYYRYPEQMKVFAREV--GATVQVAGGVPAMCDGVTQGQPGMEESLFSRDVIALA 137
           L  H  ++    QM+  A+E+     +  A  V   CDG +QG  GM +SL  R+  A+ 
Sbjct: 83  LGYHTGHWEIGMQMQAAAKEITRNGGIPFAAFVSDPCDGRSQGTHGMFDSLPYRNDAAIV 142

Query: 138 TSVSLSHGMFEGAALLGI--CDKIVPGLLMGALRFGHLPTILVPSG---PMTTGIPNKEK 192
               L   +    A++G+  CDK +P  ++       LPTILVP G   P T G    + 
Sbjct: 143 FR-RLIRSLPTRRAVIGVATCDKGLPATMIALAAMHDLPTILVPGGATLPPTVGEDAGKV 201

Query: 193 IRIRQLYAQGKIGQKELLDMEA-ACYHAEGTCTFYGTANTNQMVMEVLGLHMPGSAFVTP 251
             I   +A  ++  +E  ++   AC    G C F GTA T+Q+V E LGL +P SA    
Sbjct: 202 QTIGARFANHELSLQEAAELGCRACASPGGGCQFLGTAGTSQVVAEALGLALPHSALAPS 261

Query: 252 GTPLRQALTRAAVHRVAELGWKGDDYRPLGKIIDEKSIVNAIVGLLATGGSTNHTMHIPA 311
           G  +   + R +   V+EL  +G   R    I+ +K+I NA+V   A GGSTN  +HIPA
Sbjct: 262 GQAVWLEIARQSARAVSELDSRGITTR---DILSDKAIENAMVIHAAFGGSTNLLLHIPA 318

Query: 312 IARAAG-VIVNWNDFHDLSEVVPLIARIYPNGP---RDINEFQNAGGMAYVIKELLSANL 367
           IA AAG  I +   +  ++  VP +  + PNGP     +  F  AGG+  V+  L    L
Sbjct: 319 IAHAAGCTIPDVEHWTRINRKVPRLVSVLPNGPDYHPTVRAFL-AGGVPEVMLHLRDLGL 377

Query: 368 LNRDVTTI----AKGGIEEYAKAPALNDAGELVWKPAGEPGDDTILRPVSNPFAKDGGLR 423
           L+ D  T+        +E +  +       + + +  G   DD IL P     AK  GL 
Sbjct: 378 LHLDAMTVTGQTVGENLEWWQASERRARFRQCLREQDGVEPDDVILPPEK---AKAKGLT 434

Query: 424 ----LLEGNLG--RAMYKASAVDPK------FWTIEAPVRVFSDQDDVQKAFKAGELNKD 471
                  GN+    ++ KA+A+DP        +     VRVF  +    KA K  E+ + 
Sbjct: 435 STVCFPTGNIAPEGSVIKATAIDPSVVGEDGVYHHTGRVRVFVSEAQAIKAIKREEIVQG 494

Query: 472 VIVVVRFQGPRANGMPELHKLTPALGVLQDNGYKVALVTDGRMSGATGKVPVALHVSPEA 531
            I+VV   GP   GM E ++LT AL  +   G  V+L+TD R SG +       HVSPEA
Sbjct: 495 DIMVVIGGGPSGTGMEETYQLTSALKHI-SWGKTVSLITDARFSGVSTGACFG-HVSPEA 552

Query: 532 LGGGAIGKLRDGDIVRISVE 551
           L GG IGKLRD DI+ I+V+
Sbjct: 553 LAGGPIGKLRDNDIIEIAVD 572


Lambda     K      H
   0.318    0.136    0.403 

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: 1047
Number of extensions: 60
Number of successful extensions: 7
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: 607
Length of database: 655
Length adjustment: 38
Effective length of query: 569
Effective length of database: 617
Effective search space:   351073
Effective search space used:   351073
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: 54 (25.4 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