GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF3104
          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 (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