GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21106 in Bacteroides thetaiotaomicron VPI-5482

Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate 353166 BT3640 lipoprotein releasing system ATP-binding protein (NCBI ptt file)

Query= reanno::Smeli:SM_b21106
         (365 letters)



>FitnessBrowser__Btheta:353166
          Length = 218

 Score =  139 bits (350), Expect = 7e-38
 Identities = 79/217 (36%), Positives = 122/217 (56%), Gaps = 7/217 (3%)

Query: 4   VTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIG 63
           + L+ + K +G+L+V+ GIDLE+   E +++VGPSG GK+T L+++  L+E   G + I 
Sbjct: 2   IKLEGITKSFGSLQVLKGIDLEINKGEIVSIVGPSGAGKTTLLQIMGTLDEPDAGTVAID 61

Query: 64  GRKVNDLPP------RARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEA 117
           G  V+ +        R +NI  VFQ + L P  T  EN+     IAG  ++E   R  E 
Sbjct: 62  GTVVSRMKEKELSAFRNKNIGFVFQFHQLLPEFTALENVMIPAFIAGVSSKEANERAMEI 121

Query: 118 AAILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIK 177
            A + L      +P++LSGG++QRVA+ RA++  P V L DEP  +LD   +  +     
Sbjct: 122 LAFMGLTDRASHKPNELSGGEKQRVAVARALINHPAVILADEPSGSLDTHNKEDLHQLFF 181

Query: 178 KLHARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQ 214
            L  R+  T + VTHD+  A  ++DR V M DG I++
Sbjct: 182 DLRDRLGQTFVIVTHDEGLA-KITDRTVHMVDGTIKK 217


Lambda     K      H
   0.320    0.137    0.397 

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: 153
Number of extensions: 4
Number of successful extensions: 2
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: 365
Length of database: 218
Length adjustment: 26
Effective length of query: 339
Effective length of database: 192
Effective search space:    65088
Effective search space used:    65088
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: 47 (22.7 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