GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapQ in Azospirillum brasilense Sp245

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 AZOBR_RS08660 AZOBR_RS08660 ABC transporter permease

Query= TCDB::Q52813
         (400 letters)



>FitnessBrowser__azobra:AZOBR_RS08660
          Length = 399

 Score =  381 bits (978), Expect = e-110
 Identities = 191/380 (50%), Positives = 260/380 (68%)

Query: 21  AMYDPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSLI 80
           ++ DP  R++FYQ+L + I++   W++ HNT  NL++ + A+GFGFL   A F IG+SLI
Sbjct: 20  SLSDPTVRAVFYQVLVVGIVIAVGWFLIHNTLDNLSKRSIATGFGFLDREASFGIGESLI 79

Query: 81  TFSSDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFR 140
            +    +Y RA LVG+LNTL V++ G+  AT++G LIG+ RLS NWLIAKL + YVE+ R
Sbjct: 80  DYHPRDSYGRAFLVGVLNTLKVSIIGVVLATVLGTLIGVARLSSNWLIAKLASTYVEIVR 139

Query: 141 NIPPLLVIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVIA 200
           NIPPLL +FFWY  V   +P  R+++     ++L+ RGL  P P  D     +G AL IA
Sbjct: 140 NIPPLLQLFFWYALVSESMPPVRQALNPIPGVFLSQRGLFVPVPSADPVWGTMGFALAIA 199

Query: 201 IVASIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFNLT 260
           ++  I + RWA  RQ  TGQPF     +++L++GLPL+ ++  G P   DVP    FN  
Sbjct: 200 VIGVIFLRRWAKARQERTGQPFPIGTASLSLLIGLPLIAYIAGGAPTALDVPKLQGFNFV 259

Query: 261 GGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVP 320
           GG V+ PEF ++ + L  YTA+FIAE+VR GI  V  GQ+EAA ALG+      RLVV+P
Sbjct: 260 GGVVLTPEFFAILVGLVVYTAAFIAEVVRSGILAVNWGQTEAARALGIDSGKTLRLVVLP 319

Query: 321 QALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCIWGIVYLSL 380
           QALR+I+PPLTSQYLNLTKNSSLA+AIG+ DLV++  T LNQ+GQAIE V +    YL +
Sbjct: 320 QALRVIVPPLTSQYLNLTKNSSLALAIGYPDLVSIANTTLNQTGQAIEGVAMIMGTYLVI 379

Query: 381 SILTSLFMNWFNAKMALVER 400
           S+  S+FMNW+N ++ALVER
Sbjct: 380 SLGISIFMNWYNKRIALVER 399


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: 581
Number of extensions: 20
Number of successful extensions: 1
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: 399
Length adjustment: 31
Effective length of query: 369
Effective length of database: 368
Effective search space:   135792
Effective search space used:   135792
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