GapMind for catabolism of small carbon sources

 

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

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 349829 BT0301 ATP-binding transport protein natA (Na+ ABC transporter) (NCBI ptt file)

Query= TCDB::P73650
         (240 letters)



>FitnessBrowser__Btheta:349829
          Length = 503

 Score = 67.8 bits (164), Expect = 4e-16
 Identities = 46/152 (30%), Positives = 83/152 (54%), Gaps = 6/152 (3%)

Query: 21  LQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLGSDQIVRR 80
           L+G++F I  G +  ++GPNGAGKSTL + I G+   S G I   G + T +  +++ + 
Sbjct: 232 LRGVSFEIQTG-MFGLLGPNGAGKSTLMRVICGIFEQSYGSIWINGLD-TRIYREEL-QS 288

Query: 81  GMCYVPQVCNVFGSLTVAENLDMGAFLH---QGPTQTLKDRIYTMFPKLAQRRNQRAGTL 137
            + ++PQ    + ++T  E LD  A L     G  +  +         + +R++++ G+ 
Sbjct: 289 LIGFLPQEFGTYENMTSWEFLDYQAILKGIVDGDLRRERLDYVLKAVHMYERKDEKIGSF 348

Query: 138 SGGERQMLAMGRALMLDPDLLLLDEPSAALSP 169
           SGG +Q + +   L+  P +L++DEP+A L P
Sbjct: 349 SGGMKQRIGIALILLHLPRILVVDEPTAGLDP 380


Lambda     K      H
   0.320    0.139    0.393 

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: 193
Number of extensions: 5
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: 240
Length of database: 503
Length adjustment: 29
Effective length of query: 211
Effective length of database: 474
Effective search space:   100014
Effective search space used:   100014
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