GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24000 in Pseudomonas fluorescens FW300-N2C3

Align Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale)
to candidate AO356_29765 AO356_29765 ABC transporter substrate-binding protein

Query= uniprot:B2TBJ6
         (286 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_29765
          Length = 281

 Score =  201 bits (511), Expect = 2e-56
 Identities = 112/286 (39%), Positives = 163/286 (56%), Gaps = 9/286 (3%)

Query: 1   MKVKRTTAAKTLIGAVLGAAAIFAAPAQAKDWKTVTIALEGGYAPWNLTLPGGKLGGFEP 60
           M   R   A  L+   +G A+  A P++ K      +A EG Y PWN T   G L G+E 
Sbjct: 1   MLKNRAWLALALMPMFVGIASAQALPSEIK------VATEGAYPPWNYTNADGSLTGYEI 54

Query: 61  ELVANLCERIKLQCNLVAQDWDGMIPGLQAGKFDVLMDAISITPEREKIIAFSKPYAATP 120
           EL   LCER+K++C +V+Q+W+G+IPGL  GK+D ++ ++ +T ER+K+IAFSK YA  P
Sbjct: 55  ELTHVLCERMKVKCTIVSQEWNGIIPGLTVGKYDAIIASMGVTAERKKVIAFSKSYAKAP 114

Query: 121 ATFAVADAKVLPKAAPGAGVVKLSGDPKADQPTVDALRKQLKGKTIGIQSGTVYTKFIND 180
             F       L   A       L+  P + Q  +DAL+ +LKGK IG+Q+G+  + F+ +
Sbjct: 115 NGFLTTSDNELKSLADAGNSYDLTDSPASAQAAIDALKAKLKGKVIGVQTGSTASNFVRE 174

Query: 181 GFKDIATIRVYKTSPERDLDLANGRIDASFDDVTYYAANIDKKETASIVMAGPKIGGPIW 240
            FK +  IR Y T  +  LDLANGR+D    +VT +   I+  +   +V  GP   G + 
Sbjct: 175 YFKGL-DIRDYPTFEQLALDLANGRLDIGVANVTTFKPVIEVNK-GVLVATGPTFAGGVL 232

Query: 241 GPG-EGLAFRKQDADLKAKFDTAISAALADGTVKKLSNKWFKTDVT 285
           G G   +A R+ D  L+  FD AI+A  +DGT K L+ KWF TD++
Sbjct: 233 GQGTTNIALRQGDEALRQAFDAAITAVNSDGTNKALTEKWFGTDIS 278


Lambda     K      H
   0.316    0.134    0.396 

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: 186
Number of extensions: 13
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: 286
Length of database: 281
Length adjustment: 26
Effective length of query: 260
Effective length of database: 255
Effective search space:    66300
Effective search space used:    66300
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: 47 (22.7 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