GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztB in Pseudomonas fluorescens FW300-N1B4

Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate Pf1N1B4_916 Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)

Query= CharProtDB::CH_011913
         (426 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_916
          Length = 375

 Score =  301 bits (770), Expect = 3e-86
 Identities = 177/399 (44%), Positives = 246/399 (61%), Gaps = 34/399 (8%)

Query: 31  VVLLLFLAGLVW-LLNNAYVNLEAKGKDFNFSFLWTRAGYDLAQTLIPYSNDDTHFRALI 89
           ++ ++ + G+ W L +N   NL+ +G    F FL   AG+ +AQ LI Y+  D++ R  +
Sbjct: 8   IITVVAVVGMGWYLFDNTQTNLQHRGITSGFDFLERSAGFGIAQHLIDYTESDSYARVFV 67

Query: 90  EGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNIPLLLWILLMGT 149
            GLLNTLLV+ +G ILATILG I+GV RLS+NW++A++ TVYVE FRNIP LL IL    
Sbjct: 68  IGLLNTLLVTFIGVILATILGFIVGVARLSKNWIIAKLATVYVEVFRNIPPLLQILFWYF 127

Query: 150 ILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVTNRGTNLPAPAFDHSLGVVDLGW 209
            +  T P P++                S  F D+  V++RG N+PA          D  W
Sbjct: 128 AVFLTMPGPRN----------------SHNFGDTFFVSSRGLNMPAAL------AADGFW 165

Query: 210 NLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTWWPSL-LILFAP-ISALL 267
               S+  +AI+A++  S W  +RF        EATG     +W  L L L  P + AL+
Sbjct: 166 PFVASI-VVAIVAIVLMSRWATKRF--------EATGVPFHKFWAGLALFLVIPALCALI 216

Query: 268 YGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGIQAISRGQTEA 327
           +G   H + P++  F+F GG+ ++    AL +ALT+YTAAFIAEIVR+GI+++S GQTEA
Sbjct: 217 FGAPLHWEMPELKGFNFVGGWVLIPELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEA 276

Query: 328 AYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDLRGTLGGITLN 387
           A++LGLR G T+  VI+PQALRVI+PPL SQ+LNL KNSSLA  + Y ++     G  LN
Sbjct: 277 AHSLGLRNGPTLRKVIIPQALRVIIPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLN 336

Query: 388 QTGRELECMLLMMLIYLTISLTISSLMNLYNKSIKLKER 426
           QTG+ +E + + M +YL IS++IS LMN YNK I L ER
Sbjct: 337 QTGQAIEVIAITMSVYLAISISISLLMNWYNKRIALIER 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: 374
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: 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:

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