GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natF in Phaeobacter inhibens BS107

Align Extracellular solute-binding protein, family 3 (characterized, see rationale)
to candidate GFF194 PGA1_c01980 glutamate/glutamine/aspartate/asparagine-binding protein BztA

Query= uniprot:Q31RP1
         (359 letters)



>FitnessBrowser__Phaeo:GFF194
          Length = 338

 Score =  299 bits (765), Expect = 8e-86
 Identities = 149/316 (47%), Positives = 200/316 (63%), Gaps = 3/316 (0%)

Query: 45  LNQVQARGKLLCGVEGRLPGFSFLDSQGNYSGLDVDICKAIAAALFNDPKAIEYRSLDSV 104
           L+ V+ARGKL CGV   L GF+  ++ G + G DV +C+A+AAA+  D  A+E+      
Sbjct: 25  LDDVKARGKLNCGVTTGLVGFAAPNANGEWEGFDVAVCRAVAAAVLGDSTAVEFVPTTGK 84

Query: 105 ERFPALASGEVDLLSRNTTWTLSRDAKGGNNLEFAPTTFYDGQGLMVRRNSGIQSLQDFQ 164
            RF ALASGE+D+L+RNTTWT SRD       EF    +YDGQG MV +  G+ S ++  
Sbjct: 85  TRFTALASGEIDMLARNTTWTFSRDVD--LKFEFVGVNYYDGQGFMVPKELGVSSAKELD 142

Query: 165 GKSICVETGTTSELNLADTMRELGVQYQEIKFPNSDANYAAYAQGRCEGVTSDRSQLAAR 224
           G ++C++TGTT+ELNLAD  R   + Y+ +    +      Y  G C+  T+D S LAA 
Sbjct: 143 GATVCIQTGTTTELNLADFFRSNNISYEPVPIETNAEAQQQYLAGACDVYTTDASGLAAT 202

Query: 225 RTTLSDADQHQLLDAVISKEPLSPATLNNDSPWFDVVKWVVNATIQAEEFGITQANIDQF 284
           R T  D   H LL  +ISKEPL P   + D  W DVV+W +NA + AEE G+T ANI + 
Sbjct: 203 RATFDDPSAHVLLPEIISKEPLGPLVRHGDHEWGDVVRWSLNALVAAEELGVTSANIGEM 262

Query: 285 KT-SKNPEIRRFLGLEGELGQQLGLSNDFAYRAIKAVGNYGEIYERNVGQQSPLKLNRGL 343
              ++NPEI R LG EG LG+ LGLS D+A  AI A GNYGE++ +N+G+ +P+ L RGL
Sbjct: 263 AAGTENPEINRLLGTEGTLGEMLGLSADWAKNAIGAGGNYGEVFAKNIGEDTPIGLARGL 322

Query: 344 NQLYKNGGLLYSPPFR 359
           N  +  GGLLY+PPFR
Sbjct: 323 NAQWTEGGLLYAPPFR 338


Lambda     K      H
   0.317    0.134    0.391 

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: 293
Number of extensions: 12
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: 359
Length of database: 338
Length adjustment: 29
Effective length of query: 330
Effective length of database: 309
Effective search space:   101970
Effective search space used:   101970
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