GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapJ in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_917 Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)

Query= TCDB::Q52812
         (341 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_917
          Length = 343

 Score =  400 bits (1028), Expect = e-116
 Identities = 196/343 (57%), Positives = 248/343 (72%), Gaps = 4/343 (1%)

Query: 1   MKNKLLSAAIGAAVLAVGASAASATTLSDVKAKGFVQCGVNTGLTGFAAPDASGNWAGFD 60
           M    L+    AAVL V   A +  TL  V+ KGFVQCGV+ GL GF+ PD++G   G D
Sbjct: 3   MLKSTLAIVTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVGID 62

Query: 61  VDFCKAVASAVFGDPTKVKYTPTNAKERFTALQSGEIDVLSRNTTWTINRDTALGFNFRP 120
            DFC+AVA+AVFGD TKVK++  NAKERFTALQSGEIDVLSRN+T T +RD  +G  F  
Sbjct: 63  ADFCRAVAAAVFGDATKVKFSQLNAKERFTALQSGEIDVLSRNSTMTSSRDAGMGLKFPG 122

Query: 121 -VTYYDGQGFMVRKGLNVKSALELSGAAICVQSGTTTELNLADYFKTNNLQYNPVVFENL 179
            +TYYDG GF+    L VKSA EL GA IC+Q+GTTTELN++DYF+ N L+Y P+ F+  
Sbjct: 123 FITYYDGIGFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITFDTS 182

Query: 180 PEVNAAYDAGRCDVYTTDQSGLYSLRLTLKNPDEHIILPEIISKEPLGPAVRQGDDQWFD 239
            E   + ++GRCDV T+D+S L++ R  L +P ++++LPE ISKEPLGP VR GDD+W  
Sbjct: 183 DESAKSLESGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDDEWLA 242

Query: 240 IVSWTAYALINAEEFGITQANVD-EMKNSPNPDIKRFLGSETDTKIGTDLGLTNDWAANV 298
           IV WT YAL+NAEE G+T  NV+ E K++ NPD+ R LG+  D + G DL L  DW   +
Sbjct: 243 IVRWTGYALLNAEEAGVTSKNVEAEAKSTKNPDVARMLGA--DGEYGKDLKLPKDWVVKI 300

Query: 299 IKGVGNYGEIFERNIGQGSPLKIARGLNALWNKGGIQYAPPVR 341
           +K VGNYGE+FERN+G+ +PL+I RGLNALWN GGIQYAPPVR
Sbjct: 301 VKQVGNYGEMFERNLGKDTPLQIDRGLNALWNAGGIQYAPPVR 343


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: 373
Number of extensions: 19
Number of successful extensions: 4
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: 343
Length adjustment: 29
Effective length of query: 312
Effective length of database: 314
Effective search space:    97968
Effective search space used:    97968
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