GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_917 Glutamate Aspartate
           periplasmic binding protein precursor GltI (TC
           3.A.1.3.4)
          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.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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