GapMind for catabolism of small carbon sources

 

Alignments for a candidate for crr in Shewanella oneidensis MR-1

Align PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized)
to candidate 201386 SO2236 PTS system, glucose-specific IIA component (NCBI ptt file)

Query= SwissProt::P0A283
         (169 letters)



>FitnessBrowser__MR1:201386
          Length = 169

 Score =  216 bits (551), Expect = 1e-61
 Identities = 104/168 (61%), Positives = 132/168 (78%)

Query: 1   MGLFDKLKSLVSDDKKDTGTIEIVAPLSGEIVNIEDVPDVVFAEKIVGDGIAIKPTGNKM 60
           MG   +++ LVS   +  G I + AP++GEIV IE VPDVVFAEKIVGDGIAI PTG+ +
Sbjct: 1   MGFLSRIRRLVSGQPQLAGGIMVYAPVNGEIVAIEKVPDVVFAEKIVGDGIAIAPTGSTI 60

Query: 61  VAPVDGTIGKIFETNHAFSIESDSGIELFVHFGIDTVELKGEGFKRIAEEGQRVKVGDPV 120
           VAP+DGTIGKIFETNHAFSIES  G+ELFVHFG+ TVEL+G GF R+AEEGQ VKVGDP+
Sbjct: 61  VAPIDGTIGKIFETNHAFSIESPQGLELFVHFGVGTVELRGRGFSRLAEEGQEVKVGDPI 120

Query: 121 IEFDLPLLEEKAKSTLTPVVISNMDEIKELIKLSGSVTVGETPVIRIK 168
           + FDL  L+++  S LTPVV++NM+++K L K  GSVT G+ P+  ++
Sbjct: 121 LSFDLEYLKDQVDSLLTPVVLANMEDVKYLDKAQGSVTAGKDPIFTVQ 168


Lambda     K      H
   0.315    0.139    0.377 

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: 146
Number of extensions: 3
Number of successful extensions: 1
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: 169
Length of database: 169
Length adjustment: 18
Effective length of query: 151
Effective length of database: 151
Effective search space:    22801
Effective search space used:    22801
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: 42 (21.9 bits)
S2: 43 (21.2 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