GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Sinorhizobium meliloti 1021

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate SM_b20301 SM_b20301 dehydgrogenase

Query= BRENDA::I7A144
         (352 letters)



>FitnessBrowser__Smeli:SM_b20301
          Length = 376

 Score =  179 bits (455), Expect = 8e-50
 Identities = 122/341 (35%), Positives = 174/341 (51%), Gaps = 36/341 (10%)

Query: 23  VEEVVGGLEVPWALAFLPDGGMLIAERPGRIRLFR-EGRLSTYAE-LP-VYHRGESGLLG 79
           VE   GGLE PW  A LPDG ML+ ERPGR+RL   EG +    E +P V+ +G+ GLL 
Sbjct: 39  VEVFAGGLEHPWGAALLPDGDMLVTERPGRLRLVSAEGAVGEPIEGVPDVFAQGQGGLLD 98

Query: 80  LALHPRFPEAPYVY-AYRTVAEGGLRNQVVRLRHLGERGVLD--RVVLDGIPARPHGLHS 136
           +AL P F     VY ++    EGG    V R R   +   L   +++    PA     H 
Sbjct: 99  VALDPDFATNRTVYLSFAEEREGGAATSVGRGRLNDDATALSDFKIIFRQEPAASGENHF 158

Query: 137 GGRIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEPAPGNPFLGRRGARPEV 196
           G R+AF PDG L++T GE ++ + AQD A+  G I+RL P+G     NPF+GR GA  E+
Sbjct: 159 GSRLAFAPDGKLFITLGERFDMQEAQDPANHLGTIVRLNPDGSIPDDNPFVGREGA-DEI 217

Query: 197 YSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWP---------- 246
           +S GHRN Q  A HP+T  L+++E GP      G DE+N+   G NYGWP          
Sbjct: 218 WSYGHRNVQSAAIHPETDVLWTAEMGP-----MGGDELNIPEAGKNYGWPAVSWGRHYTG 272

Query: 247 -RVVGRGNDPRYRDPLYFWPQGFPPGNLAFF--------RGDLYVAGLRGQALLRLVLEG 297
            R+    + P +   ++ W     P  + F+        RGDL + GL    ++R+  +G
Sbjct: 273 ERIPDPPSRPEFAGSIHSWTPVISPSGMMFYTGDLFADWRGDLLIGGLSVGGIVRVQTDG 332

Query: 298 ERGRWRVLRVETALSGFGRLREVQVGPDGALYVTTSNRDGR 338
           ++     +  E  LS   R+R++    DG++        GR
Sbjct: 333 QK-----VTGEEVLSLEARIRDLLQASDGSVLALIDAASGR 368


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: 502
Number of extensions: 35
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: 376
Length adjustment: 29
Effective length of query: 323
Effective length of database: 347
Effective search space:   112081
Effective search space used:   112081
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