GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoD in Escherichia coli BW25113

Align galactonate dehydratase (EC 4.2.1.6) (characterized)
to candidate 15702 b1581 predicted dehydratase (NCBI)

Query= BRENDA::G3Y8T6
         (383 letters)



>FitnessBrowser__Keio:15702
          Length = 404

 Score =  174 bits (441), Expect = 4e-48
 Identities = 122/379 (32%), Positives = 187/379 (49%), Gaps = 44/379 (11%)

Query: 19  VKVTDSEDKFGWGEATLEGHTQAVEGAL-DEIIGRIVGYEADDIEHVWQTIWRLGFYRGG 77
           +K+T  +   G G+ATL G   +V   L D +  +++G +A  IE +WQ  ++  ++R G
Sbjct: 20  LKITTEDGITGLGDATLNGRELSVASYLQDHLCPQLIGRDAHRIEDIWQFFYKGAYWRRG 79

Query: 78  PVFMSALSGIDIALWDLKGRRLNVPVYQLLGGKVRNKVQVYAWIGG--------DRPSDV 129
           PV MSA+S +D+ALWD+K +  N+P+YQLLGG  R  V VY    G        D     
Sbjct: 80  PVTMSAISAVDMALWDIKAKAANMPLYQLLGGASREGVMVYCHTTGHSIDEALDDYARHQ 139

Query: 130 EVAAKA-RIAQGLKCVKMN-------------AT-----EDMNWLDSPSVLDSCIERIKQ 170
           E+  KA R+  G+  +K               AT     E+  W  +   LD   +    
Sbjct: 140 ELGFKAIRVQCGIPGMKTTYGMSKGKGLAYEPATKGQWPEEQLW-STEKYLDFMPKLFDA 198

Query: 171 VK-ALGLDAGL--DFHGRLHRPMAKQLAKALEPYRPLFIEEPLLVEHPEAIKQLSQHTTI 227
           V+   G +  L  D H RL    A +  K++E YR  ++E+P   E+ E  + + QHT  
Sbjct: 199 VRNKFGFNEHLLHDMHHRLTPIEAARFGKSIEDYRMFWMEDPTPAENQECFRLIRQHTVT 258

Query: 228 PIAFGERLYTRWDVKRFLEDASVDVLQPDIAHAGGISETKRIATMAETYDVAIAPHCP-- 285
           PIA GE   + WD K+ +E+  +D ++  + HAGGI+  +RIA  A  Y V    H P  
Sbjct: 259 PIAVGEVFNSIWDCKQLIEEQLIDYIRTTLTHAGGITGMRRIADFASLYQVRTGSHGPSD 318

Query: 286 LGPIALAASMQVALSTPNFVIQEMSLGMHYNVEAGDIDLTSYLTNPTVFNIEEGYVPAPT 345
           L P+ +AA++   L  PNF +QE    M Y+ +  ++        P  +  + GY+    
Sbjct: 319 LSPVCMAAALHFDLWVPNFGVQEY---MGYSEQMLEV-------FPHNWTFDNGYMHPGD 368

Query: 346 GAGLGVEIDEELVRRISRE 364
             GLG+E DE+L  +   E
Sbjct: 369 KPGLGIEFDEKLAAKYPYE 387


Lambda     K      H
   0.320    0.138    0.425 

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: 412
Number of extensions: 25
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 383
Length of database: 404
Length adjustment: 31
Effective length of query: 352
Effective length of database: 373
Effective search space:   131296
Effective search space used:   131296
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 (21.8 bits)
S2: 50 (23.9 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