GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24000 in Magnetovibrio blakemorei MV-1

Align Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale)
to candidate WP_139134956.1 BEN30_RS09695 transporter substrate-binding domain-containing protein

Query= uniprot:B2TBJ6
         (286 letters)



>NCBI__GCF_001746755.1:WP_139134956.1
          Length = 244

 Score =  128 bits (322), Expect = 1e-34
 Identities = 92/267 (34%), Positives = 128/267 (47%), Gaps = 33/267 (12%)

Query: 17  LGAAAIFAAPAQAKDWKTVTIALEGGYAPWNLTLPGGKLGGFEPELVANLCERIKLQCNL 76
           +   ++ A  A A     + I  EG Y P+NL    G+L GF+ ++   LC  +K +C  
Sbjct: 3   IATLSVIALTATAYAADKLRIGTEGAYPPFNLVDSNGELQGFDVDIAKALCASMKAECTF 62

Query: 77  VAQDWDGMIPGLQAGKFDVLMDAISITPEREKIIAFSKPYAATPATFAVADAKVLPKAAP 136
           V QDWDGMIP L   KFD ++ ++SIT ER+K + FS+ Y      F             
Sbjct: 63  VKQDWDGMIPALNKRKFDAIVASMSITEERQKAVDFSERYYTNKLQF------------- 109

Query: 137 GAGVVKLSGDPKADQPTVDALRKQLKGKTIGIQSGTVYTKFINDGFKDIATIRVYKTSPE 196
              V K   D       VD     LKGK IG Q  T+  +++     D A I++Y T   
Sbjct: 110 ---VGKKGMD-------VDISAAGLKGKVIGAQRATISGQWLEQNRAD-ADIKLYDTQEN 158

Query: 197 RDLDLANGRIDASFDD--VTYYAANIDKKETASIVMAGPKIGGPIW-GPGEGLAFRKQDA 253
             LDLA+GR+DA   D  V Y   N D         A    G P++ G   G+A RK + 
Sbjct: 159 AYLDLASGRLDAILADAFVNYEWLNSDAGN------AFEAKGDPVFDGDLIGIAIRKGED 212

Query: 254 DLKAKFDTAISAALADGTVKKLSNKWF 280
           DL+ K + AI   +ADGT  K++ K+F
Sbjct: 213 DLRIKLNKAIKDIVADGTYGKINAKYF 239


Lambda     K      H
   0.316    0.134    0.396 

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: 161
Number of extensions: 4
Number of successful extensions: 3
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: 286
Length of database: 244
Length adjustment: 25
Effective length of query: 261
Effective length of database: 219
Effective search space:    57159
Effective search space used:    57159
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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