GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aapJ in Pseudomonas stutzeri RCH2

Align AapJ, 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 GFF3104 Psest_3163 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain

Query= TCDB::Q52812
         (341 letters)



>lcl|FitnessBrowser__psRCH2:GFF3104 Psest_3163 ABC-type amino acid
           transport/signal transduction systems, periplasmic
           component/domain
          Length = 342

 Score =  430 bits (1105), Expect = e-125
 Identities = 204/336 (60%), Positives = 258/336 (76%), Gaps = 4/336 (1%)

Query: 8   AAIGAA-VLAVGASAASATTLSDVKAKGFVQCGVNTGLTGFAAPDASGNWAGFDVDFCKA 66
           A +GAA +L +   A +  TL  V+ KGFVQCG++ GL GF+  DA G + G DVD C+A
Sbjct: 9   AVLGAASLLGISGLAQAGATLDAVQKKGFVQCGISDGLPGFSFADAKGKYQGIDVDICRA 68

Query: 67  VASAVFGDPTKVKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFNFRPVTYYDG 126
           VA+AVFGD +KVKY+P  AKERFTALQSGE+DVLSRNTTWT +RD A+G NF  VTYYDG
Sbjct: 69  VAAAVFGDASKVKYSPLTAKERFTALQSGEVDVLSRNTTWTSSRDAAMGLNFTGVTYYDG 128

Query: 127 QGFMVRKGLNVKSALELSGAAICVQSGTTTELNLADYFKTNNLQYNPVVFENLPEVNAAY 186
           QGF+V K L V SA EL GA +C+Q+GTTTELNL+DYF+ N  +Y P+ ++   E   + 
Sbjct: 129 QGFLVNKELGVSSAKELDGATVCIQAGTTTELNLSDYFRANGHKYTPITYDTSDESAKSL 188

Query: 187 DAGRCDVYTTDQSGLYSLRLTLKNPDEHIILPEIISKEPLGPAVRQGDDQWFDIVSWTAY 246
           ++GRCDV T+DQS LY+ R+ L  P ++++LPE+ISKEPLGPAVRQGD++WFDIV WT +
Sbjct: 189 ESGRCDVLTSDQSQLYAQRIKLAKPADYVVLPEVISKEPLGPAVRQGDEEWFDIVRWTLF 248

Query: 247 ALINAEEFGITQANVDEM-KNSPNPDIKRFLGSETDTKIGTDLGLTNDWAANVIKGVGNY 305
           A++NAEE G+T ANV+EM K++ NPD+ R LG+E +   G DL L  DWA  ++K VGNY
Sbjct: 249 AMLNAEELGVTSANVEEMAKSTKNPDVARLLGAEGE--YGKDLKLPKDWAVQIVKQVGNY 306

Query: 306 GEIFERNIGQGSPLKIARGLNALWNKGGIQYAPPVR 341
           GEIF+RN+G GS LKI RGLNALWN GG+QYAPPVR
Sbjct: 307 GEIFDRNVGAGSELKIERGLNALWNNGGLQYAPPVR 342


Lambda     K      H
   0.316    0.134    0.398 

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: 395
Number of extensions: 20
Number of successful extensions: 3
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: 341
Length of database: 342
Length adjustment: 29
Effective length of query: 312
Effective length of database: 313
Effective search space:    97656
Effective search space used:    97656
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 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, 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