GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PA5505 in Pseudomonas fluorescens FW300-N2E3

Align Probable TonB-dependent receptor, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate AO353_22185 AO353_22185 metal ABC transporter substrate-binding protein

Query= TCDB::Q9HT68
         (260 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_22185
          Length = 271

 Score =  200 bits (509), Expect = 2e-56
 Identities = 116/260 (44%), Positives = 161/260 (61%), Gaps = 16/260 (6%)

Query: 4   LLAAFSAVAALGLTAAQAAESLTVAATPVPHAEILNVVKPLLAKEGVDLKIKEFTDYVQP 63
           L+A+FSA+A          E L VAA PVPHA+IL  V+ +  +  ++LK+ E  + V  
Sbjct: 15  LVASFSALAL---------EPLRVAADPVPHAQILAYVQKIDPQ--LNLKVIEIPNGVNS 63

Query: 64  NVQVSEKRLDANFFQHQPYLDEFNKAKGTDLVAVTGVHIEPLGAYSSKYKKLDELPSGAT 123
           N  +    +DAN+FQH PYL    +A G  L     VHIEPLG YS ++K   ++P   T
Sbjct: 64  NELLVHGDVDANYFQHLPYLKSQEQALGKKLEVAATVHIEPLGIYSHRHKSFAQVPQKGT 123

Query: 124 VVIPNDATNGGRALLLLDKAGVIKLK----DNKSITATPKDIVDNPKNIKIRELEAATLP 179
           V +PN+ TN  RAL LL   G+IKLK    D  +  ATPKDI +NPK +KI E+E+  +P
Sbjct: 124 VAVPNNVTNLSRALYLLQDNGLIKLKAGFNDPATDQATPKDIAENPKQLKILEIESPQIP 183

Query: 180 RVLTQVDMALINTNYALEAKLNPTKDALAIEGSD-SPYVNILVARPDNKDSDAMQKLAKA 238
           R L  VD+A+IN NYALEA L P KDAL +E ++ +PY NILV  P  +D   +++LAK 
Sbjct: 184 RALDDVDLAVINGNYALEAGLVPAKDALGLEKAEHNPYANILVTTPTLRDDPRIKQLAKD 243

Query: 239 LHSAEIKQFIQEKYKGAVVP 258
           L S ++ +FI + + G+V+P
Sbjct: 244 LTSPQVTKFITDNFSGSVIP 263


Lambda     K      H
   0.314    0.131    0.354 

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: 215
Number of extensions: 15
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: 260
Length of database: 271
Length adjustment: 25
Effective length of query: 235
Effective length of database: 246
Effective search space:    57810
Effective search space used:    57810
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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