GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Escherichia coli BW25113

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate 14962 b0837 predicted dehydrogenase (NCBI)

Query= BRENDA::I7A144
         (352 letters)



>FitnessBrowser__Keio:14962
          Length = 371

 Score =  169 bits (429), Expect = 8e-47
 Identities = 123/365 (33%), Positives = 183/365 (50%), Gaps = 42/365 (11%)

Query: 6   FLVGLLGLGLARGQG---LRVEEVVGGLEVPWALAFLPDG-GMLIAERPGRIRLFREGR- 60
           FLV L+ L  A       + VE +   L+ PWALAFLPD  GMLI  R G +R ++ G+ 
Sbjct: 7   FLVPLICLSSALWAAPATVNVEVLQDKLDHPWALAFLPDNHGMLITLRGGELRHWQAGKG 66

Query: 61  -LSTYAELP-VYHRGESGLLGLALHPRFPEAPYVY-AYRTVAEGGLRNQVVRLRHLGE-- 115
             +  + +P V+  G+ GLL + L P F ++  ++ +Y  V + G     V    L +  
Sbjct: 67  LSAPLSGVPDVWAHGQGGLLDVVLAPDFAQSRRIWLSYSEVGDDGKAGTAVGYGRLSDDL 126

Query: 116 RGVLD-RVVLDGIPARPHGLHSGGRIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRL 174
             V D R V   +P    G H GGR+ F   G L++  GE  +R  AQDL  L GK++RL
Sbjct: 127 SKVTDFRTVFRQMPKLSTGNHFGGRLVFDGKGYLFIALGENNQRPTAQDLDKLQGKLVRL 186

Query: 175 TPEGEPAPGNPFLGRRGARPEVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEV 234
           T +GE    NPF+   GAR E++S G RNPQG+A +P +  L+ +EHGP      G DE+
Sbjct: 187 TDQGEIPDDNPFIKESGARAEIWSYGIRNPQGMAMNPWSNALWLNEHGPR-----GGDEI 241

Query: 235 NLIVPGGNYGWPRVVGRGNDPRYR-------------DPLYFWPQGFPPGNLAFFRGD-- 279
           N+   G NYGWP      N   ++              P+++W        +AF+  D  
Sbjct: 242 NIPQKGKNYGWPLATWGINYSGFKIPEAKGEIVAGTEQPVFYWKDSPAVSGMAFYNSDKF 301

Query: 280 ------LYVAGLRGQALLRLVLEGERGRWRVLRVETALSGFG-RLREVQVGPDGALYVTT 332
                 L++  L+ + ++ + + G+    +V      L+  G R+R+V+ GPDG LYV T
Sbjct: 302 PQWQQKLFIGALKDKDVIVMSVNGD----KVTEDGRILTDRGQRIRDVRTGPDGYLYVLT 357

Query: 333 SNRDG 337
               G
Sbjct: 358 DESSG 362


Lambda     K      H
   0.322    0.146    0.460 

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: 422
Number of extensions: 28
Number of successful extensions: 6
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: 352
Length of database: 371
Length adjustment: 29
Effective length of query: 323
Effective length of database: 342
Effective search space:   110466
Effective search space used:   110466
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: 49 (23.5 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