GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztB in Escherichia coli BW25113

Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate 14790 b0653 glutamate and aspartate transporter subunit (NCBI)

Query= CharProtDB::CH_011913
         (426 letters)



>FitnessBrowser__Keio:14790
          Length = 224

 Score = 92.0 bits (227), Expect = 2e-23
 Identities = 62/199 (31%), Positives = 105/199 (52%), Gaps = 8/199 (4%)

Query: 218 LAILAVMSASFWGWRRFMARAKAVQEATGTRPTTWWPSLLI-LFAPISALLYGLGFHLDY 276
           + + AV+    WG         AV   +   P  W+    + +F  I  ++  L F+L  
Sbjct: 26  ITVTAVVIGILWG------TMLAVMRLSSFAPVAWFAKAYVNVFRSIPLVMVLLWFYLIV 79

Query: 277 PQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGIQAISRGQTEAAYALGLRPG 336
           P   +       +      + ++A +++ AA+ +EI+RAGIQ+ISRGQ+ AA ALG+   
Sbjct: 80  PGFLQNVLGLSPKNDIRLISAMVAFSMFEAAYYSEIIRAGIQSISRGQSSAALALGMTHW 139

Query: 337 RTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDLRGTLGGITLNQTGRELECM 396
           ++M L+ILPQA R +VP L++Q + L +++SL   +S  D   T   I   + G ++E +
Sbjct: 140 QSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVLSLADFFRTASTIG-ERDGTQVEMI 198

Query: 397 LLMMLIYLTISLTISSLMN 415
           L    +Y  ISL+ S L++
Sbjct: 199 LFAGFVYFVISLSASLLVS 217



 Score = 47.4 bits (111), Expect = 4e-10
 Identities = 34/88 (38%), Positives = 48/88 (54%), Gaps = 6/88 (6%)

Query: 88  LIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNIPL---LLWI 144
           L++GL+ TL ++V   ++  + GT++ V+RLS    VA     YV  FR+IPL   LLW 
Sbjct: 16  LLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYVNVFRSIPLVMVLLWF 75

Query: 145 LLM--GTILAETRPVPK-DFRLTEAMKA 169
            L+  G +       PK D RL  AM A
Sbjct: 76  YLIVPGFLQNVLGLSPKNDIRLISAMVA 103


Lambda     K      H
   0.326    0.139    0.419 

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: 203
Number of extensions: 8
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 426
Length of database: 224
Length adjustment: 27
Effective length of query: 399
Effective length of database: 197
Effective search space:    78603
Effective search space used:    78603
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 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