GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aapQ in Pseudomonas putida KT2440

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 PP_1298 PP_1298 putative amino acid ABC transporter - permease subunit

Query= TCDB::Q52813
         (400 letters)



>lcl|FitnessBrowser__Putida:PP_1298 PP_1298 putative amino acid ABC
           transporter - permease subunit
          Length = 392

 Score =  382 bits (982), Expect = e-111
 Identities = 194/381 (50%), Positives = 256/381 (67%), Gaps = 1/381 (0%)

Query: 21  AMYDPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSLI 80
           ++ DP+ R+  +QILTIV +VG  W++ HNT  NL      SGF FL   AGF I Q LI
Sbjct: 12  SLNDPRVRAWLFQILTIVFVVGLGWYLFHNTQTNLQHRGITSGFDFLDRSAGFGIAQHLI 71

Query: 81  TFSSDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFR 140
            +    +YAR  ++G+LNTLLV   G+  ATI+GF+IG+ RLS NW+I KL TVYVE FR
Sbjct: 72  PYVESDSYARVFVIGLLNTLLVTFIGVILATILGFIIGVARLSPNWMINKLATVYVETFR 131

Query: 141 NIPPLLVIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVIA 200
           NIPPLL I FWY  V   LP PR S+ +    +++NRGL  P      G     +AL +A
Sbjct: 132 NIPPLLQILFWYFAVFLTLPGPRGSINIEDMFFISNRGLNMPGASIADGFWPFVVALALA 191

Query: 201 IVASIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFNLT 260
           I A  ++ R+A+KR   TG PFH  W  + L + +P L  ++ G P+T+D+P    FN  
Sbjct: 192 IAAIALMVRYANKRFNETGVPFHKFWAGLLLFIAIPSLSVLLFGSPVTWDMPQLKGFNFV 251

Query: 261 GGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVP 320
           GG V+ PE ++L LAL+ YTA+FIAEIVR GIR V  GQ+EAA +LGL      R V++P
Sbjct: 252 GGWVLIPELLALTLALTIYTAAFIAEIVRSGIRSVSHGQTEAARSLGLREGPTLRKVIIP 311

Query: 321 QALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAV-GGTILNQSGQAIEIVCIWGIVYLS 379
           QALR+IIPPLTSQYLNL KNSSLA  IG+ ++V++  GT+LNQ+GQAIE++ I   VYL+
Sbjct: 312 QALRVIIPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLA 371

Query: 380 LSILTSLFMNWFNAKMALVER 400
           +SI  SL MNW+N ++AL+ER
Sbjct: 372 ISISISLLMNWYNKRIALIER 392


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: 496
Number of extensions: 18
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: 392
Length adjustment: 31
Effective length of query: 369
Effective length of database: 361
Effective search space:   133209
Effective search space used:   133209
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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