GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Sinorhizobium meliloti 1021

Align gluconolactonase subunit (EC 3.1.1.17) (characterized)
to candidate SM_b20453 SM_b20453 gluconolactonase

Query= metacyc::MONOMER-13276
         (356 letters)



>FitnessBrowser__Smeli:SM_b20453
          Length = 303

 Score =  148 bits (374), Expect = 2e-40
 Identities = 103/311 (33%), Positives = 156/311 (50%), Gaps = 32/311 (10%)

Query: 54  RLDAILDVSTPIEVIASDIQWSEGPVWVKNGNFLLFSDPPANIMRKWTPDAGVSIFLKPS 113
           R  +++  S  +E +    +W+EGPVW  + + L++SD P   M +WTPD G S+F  PS
Sbjct: 13  RFRSLIVGSAALEELYRGCRWAEGPVWFSDLDCLIWSDIPNQRMMRWTPDGGASVFRSPS 72

Query: 114 GHAEPIPAGQFREPGSNGMKVGPDGKIWVADSGTRAIMKVDPVTRQRSVVVDNYKGKRFN 173
            +              NG     +G++   + G R + + +   R  +V+ D Y+GKR N
Sbjct: 73  NYV-------------NGNTRDREGRLISCEHGGRRVTRTEHDGR-ITVLADIYEGKRLN 118

Query: 174 SPNDLFFSKSGAVYFTDPPYGLTNLDESDIKEMNY--NGVFRLSP-DGRLDLIEAGLSRP 230
           SPND      G+++FTDP YG+ +  E    E       V+R+ P  G +  +     +P
Sbjct: 119 SPNDAVVHSDGSIWFTDPTYGILSDYEGHKAEPEQPTRNVYRIDPLSGAIKAVVRDFIQP 178

Query: 231 NGLALSPDETKLYVSNSDRAS----PNIWVYSLDSNGLPTSRTLLRNFRKEYFDQGLAGL 286
           NGLA SPDE +LY+++S  A      +I V+ + ++G      +L N R  YF     G 
Sbjct: 179 NGLAFSPDEARLYIADSGSAKHEVPSHIRVFDVAADG------VLANDR--YFCSIDNGN 230

Query: 287 PDGMNIDKQGNLFASAPGGIYIFAPDGECLGLISGNPGQPLSNCCF-GEKGQTLFISASH 345
           PDG   D  GNL+ SA  G++ F   G  LG I     Q +SN  F G K   LFI+A+ 
Sbjct: 231 PDGFRFDVAGNLWCSAADGVHCFDTGGTLLGKIL--VPQTVSNLTFGGPKKNRLFITATQ 288

Query: 346 NVVRVRTKTFG 356
           ++  + T T G
Sbjct: 289 SLYSIYTATNG 299


Lambda     K      H
   0.317    0.135    0.409 

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: 410
Number of extensions: 26
Number of successful extensions: 4
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: 356
Length of database: 303
Length adjustment: 28
Effective length of query: 328
Effective length of database: 275
Effective search space:    90200
Effective search space used:    90200
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 (21.6 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