GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztB in Marinobacter adhaerens HP15

Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate GFF2245 HP15_2195 amino acid ABC transporter, permease protein

Query= CharProtDB::CH_011913
         (426 letters)



>FitnessBrowser__Marino:GFF2245
          Length = 395

 Score =  287 bits (735), Expect = 3e-82
 Identities = 177/410 (43%), Positives = 237/410 (57%), Gaps = 33/410 (8%)

Query: 19  YDTRFRSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFLWTRAGYDLAQTLIPY 78
           YD R RS+  Q V + L   G   L++N   N+E++G    F FL   AG+ +   L+PY
Sbjct: 17  YDPRVRSLFFQAVAIALVFWGGWILVDNTLSNMESRGISTGFGFLGETAGFGIIMNLVPY 76

Query: 79  SNDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNI 138
               ++ R    GL NTLLVS +G + ATILG IIGV RLS NWLVA++  VY+E  RNI
Sbjct: 77  DATMSYGRTFWVGLTNTLLVSAMGVVAATILGFIIGVARLSSNWLVAKMALVYIEVIRNI 136

Query: 139 PLLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVTNRGTNLPAPAF 198
           PLLL I      +    P P+     +++   G           ++ + NRG  LP P  
Sbjct: 137 PLLLQIFFWYFAVLSNLPSPR-----QSVDVGG-----------ALFLNNRGLYLPDPVT 180

Query: 199 DHSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTW--WPSL 256
               G+V  G         LAI AV+    W        AK  Q ATG    T+    ++
Sbjct: 181 QEGFGIVWGGI-------LLAIAAVVGIRIW--------AKKRQLATGQIFPTFKVGVAI 225

Query: 257 LILFAPISALLYGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAG 316
           L+L   IS L+ G     D P +  F+F GG  ++    AL IAL+LYTA+FIAEIVR+G
Sbjct: 226 LVLVPIISYLVAGRPLEWDLPALRGFNFGGGITIIPELAALWIALSLYTASFIAEIVRSG 285

Query: 317 IQAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMD 376
           I ++S+GQTEA+ ALGL  G T+ LV++PQA+RVI+PPL SQ+LNL KNSSLA A+ Y D
Sbjct: 286 ILSVSKGQTEASKALGLPNGLTLRLVVIPQAMRVIIPPLTSQYLNLVKNSSLATAIGYPD 345

Query: 377 LRGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSIKLKER 426
           L     G TLNQTG+ +E + + M +YLTISL IS  MN+YN+++ +KER
Sbjct: 346 LVAVFMGTTLNQTGQAVEVVAITMAVYLTISLLISLFMNIYNRAVAIKER 395


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: 435
Number of extensions: 23
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: 426
Length of database: 395
Length adjustment: 31
Effective length of query: 395
Effective length of database: 364
Effective search space:   143780
Effective search space used:   143780
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: 50 (23.9 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