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 SMc01583 SMc01583 hypothetical protein

Query= BRENDA::I7A144
         (352 letters)



>FitnessBrowser__Smeli:SMc01583
          Length = 396

 Score =  179 bits (453), Expect = 1e-49
 Identities = 123/340 (36%), Positives = 169/340 (49%), Gaps = 33/340 (9%)

Query: 23  VEEVVGGLEVPWALAFLPDGGMLIAERPGRIRLFREGRLSTYAE-LPVYH-RGESGLLGL 80
           VE +  GLE PWA+  +PDG +++ ERPGR+R+ R+G+LS   + +P     G+ GLL +
Sbjct: 54  VETLASGLEHPWAVEAMPDGALIVTERPGRLRILRDGKLSAAIKGVPTAAAHGQGGLLDV 113

Query: 81  ALHPRFPEAPYVYAYRTV-AEGGLRNQVVRLRHLGERGVLDRV--VLDGIPARPHGLHSG 137
           AL  +F     +Y   +V  +GG    +VR     +   L  V  +         G H G
Sbjct: 114 ALDRQFATNRTLYLTLSVRGDGGYGTVLVRAALSQDEQSLTEVKEIFRMNKFTRKGQHFG 173

Query: 138 GRIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEPAPGNPFLGRRGARPEVY 197
            RIA   DG L+   G+  E E AQD     G IL +  +G     NP+ G  G   E++
Sbjct: 174 SRIAIDKDGSLFFGIGDRGEGERAQDSRDHAGSILHINADGSIPASNPYRGGTGGLAEIW 233

Query: 198 SLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWPRV--------- 248
           S+GHRNPQG+ + P+ G+L + EHG       G DEVN   PG NYGWP +         
Sbjct: 234 SIGHRNPQGITFDPEGGKLLTVEHG-----ARGGDEVNNPQPGKNYGWPVITFGKDYSGV 288

Query: 249 -VGRGNDPR-YRDPLYFWPQGFPPGNLAFFR--------GDLYVAGLRGQALLRLVLEGE 298
            +G G        PL++W     PG +A +R        GDL +A L+ Q L RL  + E
Sbjct: 289 EIGEGTAKEGLEQPLFYWDPSIAPGAIAVYRGSMFPEWNGDLLIAALKYQLLARLDRD-E 347

Query: 299 RGRWRVLRVETALSG-FGRLREVQVGPDGALYVTTSNRDG 337
            G   V   E    G FGR+R+V V  DGAL + T   DG
Sbjct: 348 TG--AVTNEERLFDGEFGRIRDVIVASDGALIMVTDEEDG 385


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: 504
Number of extensions: 27
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: 396
Length adjustment: 30
Effective length of query: 322
Effective length of database: 366
Effective search space:   117852
Effective search space used:   117852
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