GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bztA in Pseudomonas fluorescens FW300-N2E2

Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate Pf6N2E2_5402 Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)

Query= TCDB::Q52663
         (338 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5402 Glutamate Aspartate
           periplasmic binding protein precursor GltI (TC
           3.A.1.3.4)
          Length = 343

 Score =  335 bits (859), Expect = 1e-96
 Identities = 169/335 (50%), Positives = 222/335 (66%), Gaps = 5/335 (1%)

Query: 9   SVALAALVAG----AASASTLDDVKARGQLICGSNPGLTGFAAPDANGVYQGFDVAVCKA 64
           +V  AA V G    A + +TLD V+ +G + CG + GL GF+ PD+ G   G D   C+A
Sbjct: 9   AVMTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVGIDADFCRA 68

Query: 65  VAAAVLGDPMKVKYVPLTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFVA-VNYYD 123
           VAAAV GD  KVK+  L  + RFTAL SGE+D+L RNST T SRD  + L F   + YYD
Sbjct: 69  VAAAVFGDATKVKFSQLNAKERFTALQSGEIDMLSRNSTMTSSRDAGMGLKFPGFITYYD 128

Query: 124 GQGFMVNKSLGVSSAKELDGATICVQTGTTTEMNLADFFKANNMTYTPVNIADDAEGQQK 183
           G GF+ N  LGV SAKELDGATIC+Q GTTTE+N++D+F+AN + YTP+      E  + 
Sbjct: 129 GIGFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITFDTSDESAKS 188

Query: 184 FAAGACDSYTTDASGLASSRATLPNAADIVILPEIISKEPLGPVVRHGDNNWGDIVRWSF 243
             +G CD  T+D S L + R+ L +  D V+LPE ISKEPLGPVVR+GD+ W  IVRW+ 
Sbjct: 189 LESGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDDEWLAIVRWTG 248

Query: 244 YALVAAEEYGITKANLEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAILASGNYG 303
           YAL+ AEE G+T  N+E  A ST+NP++ R+LG +G+ GK + L  D+  + +   GNYG
Sbjct: 249 YALLNAEEAGVTSKNVEAEAKSTKNPDVARMLGADGEYGKDLKLPKDWVVQIVKQVGNYG 308

Query: 304 EVFEANIGASTSIGLARGLNAQWTQGGLMYAPPFR 338
           E+FE N+G  T + + RGLNA W  GG+ YAPP R
Sbjct: 309 EMFERNLGKGTPLEIDRGLNALWNAGGIQYAPPVR 343


Lambda     K      H
   0.316    0.132    0.384 

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: 324
Number of extensions: 11
Number of successful extensions: 2
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: 338
Length of database: 343
Length adjustment: 28
Effective length of query: 310
Effective length of database: 315
Effective search space:    97650
Effective search space used:    97650
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 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