GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztB in Rhizorhabdus wittichii RW1

Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate WP_012048835.1 SWIT_RS13330 ABC transporter permease subunit

Query= CharProtDB::CH_011913
         (426 letters)



>NCBI__GCF_000016765.1:WP_012048835.1
          Length = 374

 Score =  174 bits (442), Expect = 3e-48
 Identities = 124/394 (31%), Positives = 202/394 (51%), Gaps = 42/394 (10%)

Query: 31  VVLLLFLAGLVWLLNNAYV-NLEAKGKDFNFSFLWTRAGYDLAQTLIPYSNDDTHFRALI 89
           V LLL LAGLV ++      N+E +    +  FL + A + +A++ + Y+  DT   A +
Sbjct: 17  VALLLALAGLVLVVARTVSDNMERQDMVLSLGFLRSTAEFPIAESFLAYAPGDTIAWAFV 76

Query: 90  EGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNIPLLLWILLM-G 148
            GL N++ +++L  +L+T+ G  I + R S + L   +   +V+  RN+PL++ +L   G
Sbjct: 77  VGLGNSIALTLLIIVLSTMAGVPIALARHSGHMLARTLAGGFVDLVRNVPLVVQLLFWYG 136

Query: 149 TILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVTNRGTNLPAPAFDHSLGVVDLG 208
            IL    P             A  +P   ++      +TNRG  +       ++G+   G
Sbjct: 137 VILMAFPPA-----------RAAAQPLPGLF------LTNRGITVT------TVGIT--G 171

Query: 209 WNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTWWPSLLILFAPISALLY 268
             LP+ +  L  L +   +   WR  + +A      T    +  W            ++ 
Sbjct: 172 TALPMIVTVLGGLTLTLIT--AWRGHLHKASLCTLGTIVAGSALW------------IVL 217

Query: 269 GLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGIQAISRGQTEAA 328
            LG   D P   +F+FTGG  +   F A+L    +Y +AF AEIVR G+  + RGQ EA+
Sbjct: 218 DLGLARDVPHFDRFNFTGGLTLTPEFVAVLWGSVIYASAFAAEIVRGGLDGVPRGQWEAS 277

Query: 329 YALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDLRGTLGGITLNQ 388
            ALGL   +++ LVI+PQALR+IVPP+ SQF+ + KNS+LA+ V Y DL   +    +N 
Sbjct: 278 RALGLSKRQSLRLVIVPQALRMIVPPMNSQFITILKNSTLALVVGYPDL-NFVANTAINH 336

Query: 389 TGRELECMLLMMLIYLTISLTISSLMNLYNKSIK 422
           TG+ LE + ++ML++ T++  IS  MN  N  ++
Sbjct: 337 TGQGLEGVAILMLVFFTLASAISLAMNRLNARVQ 370


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: 337
Number of extensions: 15
Number of successful extensions: 2
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: 374
Length adjustment: 31
Effective length of query: 395
Effective length of database: 343
Effective search space:   135485
Effective search space used:   135485
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 Apr 09 2024. 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