GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapQ in Pseudomonas fluorescens FW300-N2E2

Align AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate Pf6N2E2_5403 Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)

Query= TCDB::Q52813
         (400 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5403
          Length = 375

 Score =  374 bits (961), Expect = e-108
 Identities = 187/374 (50%), Positives = 259/374 (69%), Gaps = 1/374 (0%)

Query: 28  RSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSLITFSSDST 87
           R+  +Q++T+V ++   W++  NT  NL      SGFGFL   AGF I Q LI ++   +
Sbjct: 2   RAWVFQVVTVVAVIALGWFLFDNTQTNLQHRGITSGFGFLERSAGFGIAQHLIDYTEADS 61

Query: 88  YARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIPPLLV 147
           YAR  L+G+LNTLLV   G+  ATI+GF+IG+ RLS+NW+I+KL TVYVEVFRNIPPLL 
Sbjct: 62  YARVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLLQ 121

Query: 148 IFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVIAIVASIII 207
           I FWY  V   +P PR +     + ++++RGL  P  +   G     I++V+AIVA +++
Sbjct: 122 ILFWYFAVFLSMPGPRAAHNFGDTFFVSSRGLNMPAALVAEGFWPFVISVVLAIVAIVLM 181

Query: 208 ARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFNLTGGSVVGP 267
            RWA+KR  ATG+PFH  W  +AL + +P L  ++ G P+ +++P    FN  GG V+ P
Sbjct: 182 TRWANKRFEATGEPFHKFWVGLALFLVIPALSALLFGAPVHWEMPELKGFNFVGGWVLIP 241

Query: 268 EFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQALRIII 327
           E ++L LAL+ YTA+FIAEIVR GI+ V  GQ+EAA +LGL      R V++PQALR+II
Sbjct: 242 ELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVII 301

Query: 328 PPLTSQYLNLTKNSSLAIAIGFSDLVAV-GGTILNQSGQAIEIVCIWGIVYLSLSILTSL 386
           PPLTSQYLNL KNSSLA  IG+ ++V++  GT+LNQ+GQAIE++ I   VYL++SI  SL
Sbjct: 302 PPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISISL 361

Query: 387 FMNWFNAKMALVER 400
            MNW+N ++AL+ER
Sbjct: 362 LMNWYNKRIALIER 375


Lambda     K      H
   0.327    0.141    0.432 

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: 483
Number of extensions: 20
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: 400
Length of database: 375
Length adjustment: 30
Effective length of query: 370
Effective length of database: 345
Effective search space:   127650
Effective search space used:   127650
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