GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztA in Pseudomonas fluorescens FW300-N2E3

Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate AO353_04615 AO353_04615 amino acid ABC transporter substrate-binding protein

Query= TCDB::Q52663
         (338 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_04615
          Length = 343

 Score =  340 bits (873), Expect = 2e-98
 Identities = 173/335 (51%), Positives = 223/335 (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   AVVTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVGIDADYCRA 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 GVGFLANSKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITFDTSDESAKS 188

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

Query: 244 YALVAAEEYGITKANLEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAILASGNYG 303
           YA++ AEE GIT  N+E  A ST+NP++ RLLG +G+ GK + L  D+  + +   GNYG
Sbjct: 249 YAMLNAEEAGITSKNVEAEAKSTKNPDVARLLGTDGEYGKDLKLPKDWVVKIVKQVGNYG 308

Query: 304 EVFEANIGASTSIGLARGLNAQWTQGGLMYAPPFR 338
           EVFE N+G ST + + RGLNA WT GG+ YAPP R
Sbjct: 309 EVFEKNLGKSTPLEIDRGLNALWTNGGIQYAPPVR 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: 319
Number of extensions: 9
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:

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