GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_1298
          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 (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