GapMind for catabolism of small carbon sources

 

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

Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_084005156.1 BEN30_RS06480 amino acid ABC transporter substrate-binding protein

Query= TCDB::Q52663
         (338 letters)



>NCBI__GCF_001746755.1:WP_084005156.1
          Length = 340

 Score =  233 bits (594), Expect = 5e-66
 Identities = 128/323 (39%), Positives = 184/323 (56%), Gaps = 9/323 (2%)

Query: 21  SASTLDDVKARGQLICGSNPGLTGFAAPDANGVYQGFDVAVCKAVAAAVLGDPMKVKYVP 80
           +AST++ VK RG ++CG    + GF+  +A+G + GF V  C+A  AAVLG+   V+   
Sbjct: 22  AASTIETVKNRGFVLCGVTDRVPGFSLHEADGSWSGFFVDFCRAAGAAVLGNADAVQIES 81

Query: 81  LTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFVAVNYYDGQGFMVNKSLGVSSAKE 140
                   AL   EVD+L   STWT  RDT   +DF  + +YDGQGF+++ +LGV S K+
Sbjct: 82  YW----LDALEGREVDILHAGSTWTLVRDTTRMIDFPGIYFYDGQGFILHSNLGVKSLKD 137

Query: 141 L----DGATICVQTGTTTEMNLADFFKANNMTYTPVNIADDAEGQQKFAAGACDSYTTDA 196
                D     +   +T   NL +F     +T+T V I       + F  G CD    D 
Sbjct: 138 AMTTKDLKVCAIGPSSTARANLEEFIANTGVTWTLVPIQTMDGMWRAFFGGRCDMAIHDR 197

Query: 197 SGLASSRA-TLPNAADIVILPEIISKEPLGPVVRHGDNNWGDIVRWSFYALVAAEEYGIT 255
           S L +  A  L ++ D V+LPE+ISKEPL P VR  D  W D++ W   A +AAE+ G+ 
Sbjct: 198 SALVAVHAGRLDDSDDYVVLPEVISKEPLAPAVRSDDVQWRDLIFWVTMATIAAEDLGVN 257

Query: 256 KANLEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAILASGNYGEVFEANIGASTS 315
           + N++++ A + +PE+RRLLG +  +G   GL +D+A + I   GNYGE+F  N+G  T 
Sbjct: 258 QDNVDDMLAHSTSPEVRRLLGADPGIGVGFGLSDDWAYQVIKQLGNYGEIFARNLGPKTQ 317

Query: 316 IGLARGLNAQWTQGGLMYAPPFR 338
             ++RGLN  W  GGL+YAPP R
Sbjct: 318 FKMSRGLNQLWRDGGLLYAPPVR 340


Lambda     K      H
   0.316    0.132    0.384 

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: 314
Number of extensions: 15
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: 338
Length of database: 340
Length adjustment: 28
Effective length of query: 310
Effective length of database: 312
Effective search space:    96720
Effective search space used:    96720
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 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