GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztB in Herbaspirillum seropedicae SmR1

Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate HSERO_RS17560 HSERO_RS17560 glutamate/aspartate transporter permease GltK

Query= CharProtDB::CH_011913
         (426 letters)



>FitnessBrowser__HerbieS:HSERO_RS17560
          Length = 227

 Score = 97.4 bits (241), Expect = 4e-25
 Identities = 72/216 (33%), Positives = 111/216 (51%), Gaps = 9/216 (4%)

Query: 207 LGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTWWPSLLI-LFAPISA 265
           LG  L VSL  + ++A++    WG    M R           P  W+ +  + LF  I  
Sbjct: 18  LGDGLLVSLK-ITLVAIVFGMVWGTLLAMMRLSRHS------PLQWFAAGYVNLFRSIPL 70

Query: 266 LLYGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGIQAISRGQT 325
           ++  L F L  PQ+ +  F          T+ L+A  L+ AA+ AEI+RAGI ++SRGQ 
Sbjct: 71  VMVLLWFFLIVPQLLQKLFGLSPANDLRMTSALVAFALFEAAYYAEIIRAGINSVSRGQM 130

Query: 326 EAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDLRGTLGGIT 385
            AAYALGL   + M +VILPQA R +VP L++Q + L +++SL    +  D  G    I 
Sbjct: 131 AAAYALGLTYPQAMGMVILPQAFRNMVPLLLTQGIVLFQDTSLVYVSALADFFGRAYSIG 190

Query: 386 LNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSI 421
             + GR +E + +   +Y  I  ++S ++  Y K +
Sbjct: 191 -ERNGRIIEMLFVAGAVYFIICFSMSLMVKRYRKKV 225



 Score = 42.7 bits (99), Expect = 1e-08
 Identities = 28/90 (31%), Positives = 48/90 (53%), Gaps = 6/90 (6%)

Query: 86  RALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNIPL---LL 142
           R L +GLL +L ++++  +   + GT++ ++RLS++  +      YV  FR+IPL   LL
Sbjct: 16  RVLGDGLLVSLKITLVAIVFGMVWGTLLAMMRLSRHSPLQWFAAGYVNLFRSIPLVMVLL 75

Query: 143 WILLMGTILAET---RPVPKDFRLTEAMKA 169
           W  L+   L +         D R+T A+ A
Sbjct: 76  WFFLIVPQLLQKLFGLSPANDLRMTSALVA 105


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: 199
Number of extensions: 12
Number of successful extensions: 4
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: 227
Length adjustment: 27
Effective length of query: 399
Effective length of database: 200
Effective search space:    79800
Effective search space used:    79800
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