GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bztB in Pseudomonas fluorescens FW300-N2E2

Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate Pf6N2E2_5403 Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)

Query= CharProtDB::CH_011913
         (426 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5403 Glutamate Aspartate
           transport system permease protein GltJ (TC 3.A.1.3.4)
          Length = 375

 Score =  300 bits (767), Expect = 6e-86
 Identities = 181/405 (44%), Positives = 250/405 (61%), Gaps = 33/405 (8%)

Query: 24  RSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFLWTRAGYDLAQTLIPYSNDDT 83
           R+   Q+V ++  +A   +L +N   NL+ +G    F FL   AG+ +AQ LI Y+  D+
Sbjct: 2   RAWVFQVVTVVAVIALGWFLFDNTQTNLQHRGITSGFGFLERSAGFGIAQHLIDYTEADS 61

Query: 84  HFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNIPLLLW 143
           + R  + GLLNTLLV+ +G ILATILG IIGV RLSQNW+++++ TVYVE FRNIP LL 
Sbjct: 62  YARVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLLQ 121

Query: 144 ILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVTNRGTNLPAPAFDHSLG 203
           IL     +  + P                 P+A+  F D+  V++RG N+PA        
Sbjct: 122 ILFWYFAVFLSMP----------------GPRAAHNFGDTFFVSSRGLNMPAAL------ 159

Query: 204 VVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTWWPSL-LILFAP 262
           V +  W   +S+  LAI+A++  + W  +RF        EATG     +W  L L L  P
Sbjct: 160 VAEGFWPFVISV-VLAIVAIVLMTRWANKRF--------EATGEPFHKFWVGLALFLVIP 210

Query: 263 -ISALLYGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGIQAIS 321
            +SALL+G   H + P++  F+F GG+ ++    AL +ALT+YTAAFIAEIVR+GI+++S
Sbjct: 211 ALSALLFGAPVHWEMPELKGFNFVGGWVLIPELLALTLALTVYTAAFIAEIVRSGIKSVS 270

Query: 322 RGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDLRGTL 381
            GQTEAA +LGLR G T+  VI+PQALRVI+PPL SQ+LNL KNSSLA  + Y ++    
Sbjct: 271 HGQTEAARSLGLRNGPTLRKVIIPQALRVIIPPLTSQYLNLAKNSSLAAGIGYPEMVSLF 330

Query: 382 GGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSIKLKER 426
            G  LNQTG+ +E + + M +YL IS++IS LMN YNK I L ER
Sbjct: 331 AGTVLNQTGQAIEVIAITMSVYLAISISISLLMNWYNKRIALIER 375


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: 373
Number of extensions: 15
Number of successful extensions: 3
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: 375
Length adjustment: 31
Effective length of query: 395
Effective length of database: 344
Effective search space:   135880
Effective search space used:   135880
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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