GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24000 in Pseudomonas fluorescens FW300-N2E3

Align Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale)
to candidate AO353_27970 AO353_27970 ABC transporter substrate-binding protein

Query= uniprot:B2TBJ6
         (286 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_27970
          Length = 258

 Score =  132 bits (333), Expect = 6e-36
 Identities = 86/274 (31%), Positives = 137/274 (50%), Gaps = 29/274 (10%)

Query: 16  VLGAAAIFAAPAQAK-DWKTVTIALEGGYAPWNLTLPGGKLGGFEPELVANLCERIKLQC 74
           +L A A  A    A  D  ++ I +E  Y P++   P G + GF+ ++   LCE +K++C
Sbjct: 6   LLAALAFCAVSTLAHADEDSLRIGIEAAYPPFSFKTPEGNISGFDYDIGNALCEEMKIKC 65

Query: 75  NLVAQDWDGMIPGLQAGKFDVLMDAISITPEREKIIAFSKPYAATPATFAVADAKVLPKA 134
             V Q++DGMIP L+  K D ++ ++SIT +R K + FS+ Y  TP  FA    + +   
Sbjct: 66  QWVIQEFDGMIPSLKVRKIDAVLSSMSITDDRLKSVDFSEKYYHTPGKFAAKAGQAI--- 122

Query: 135 APGAGVVKLSGDPKADQPTVDALRKQLKGKTIGIQSGTVYTKFINDGF--KDIATIRVYK 192
                      DPK D          LKGK +G+Q  + Y ++  +      +  +R Y 
Sbjct: 123 ----------NDPKVD----------LKGKKLGVQRSSTYDRYATEQLAPAGVEVVR-YS 161

Query: 193 TSPERDLDLANGRIDASFDDVTYYAANIDKKETAS-IVMAGPKIGGP-IWGPGEGLAFRK 250
           +  E  LDLA+GR+DA+  D+     +  K    +   + GP I  P  +G G G+A RK
Sbjct: 162 SQNEAFLDLASGRLDATLADIVNTNESFIKTPAGNGFALVGPDINDPKYFGRGAGIALRK 221

Query: 251 QDADLKAKFDTAISAALADGTVKKLSNKWFKTDV 284
            D    A+ +TAI A  A+G  +++  K+F  D+
Sbjct: 222 GDTANAARLNTAIDAIRANGKYQQVMAKYFAFDI 255


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: 177
Number of extensions: 8
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: 286
Length of database: 258
Length adjustment: 25
Effective length of query: 261
Effective length of database: 233
Effective search space:    60813
Effective search space used:    60813
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.

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:

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