GapMind for catabolism of small carbon sources

 

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

Align fructokinase; EC 2.7.1.4 (characterized)
to candidate AO356_23520 AO356_23520 fructoselysine kinase

Query= CharProtDB::CH_006622
         (307 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_23520
          Length = 284

 Score = 78.6 bits (192), Expect = 2e-19
 Identities = 77/264 (29%), Positives = 117/264 (44%), Gaps = 31/264 (11%)

Query: 3   AKVWVLGDAVVDLLPESEGRLLQCPGGAPANVAVGVARLGGNSGFIGAVGGDPFGRYMRH 62
           A +  +GD  +D+  +   + ++ PGG   NVAV  ARLG  S ++G VG D  G+Y+  
Sbjct: 2   ASLIAVGDNTLDVYLD---QTIEYPGGNALNVAVFAARLGARSAYLGCVGDDRHGQYLLD 58

Query: 63  TLQQEQVDVSHMYLDDQHRTSTVVVDLDDQGERTFTFMVRPSADLFLVEEDLPQFAAGQW 122
            LQQE VD S             V ++  +GER F       +D  +  +   +  A   
Sbjct: 59  CLQQEAVDASRCRTLSGANGWACVDNV--EGERVFL-----GSDPGVCRQ--LRLDADDL 109

Query: 123 LHVCSIALSAEPSRSTTFAAMESIRSAGGRVSFDPNIRPDLWQD---QALLLACLDRALH 179
            ++ +  L+     S     +  +R A G +SFD +   D W +   QAL        + 
Sbjct: 110 AYIGTFPLAHSSLYSGLEDQLAQVRQASGCLSFDFS---DNWVEFDWQAL--------IQ 158

Query: 180 MANVVKLSEEELVFISSSNDLAYGIASVTERYQPELLLVTRGKAGVLAAFQQKFTHFNAR 239
             +V   S  +L     S   A  +A+      P ++++TRG  G LA   Q      AR
Sbjct: 159 HVDVAFFSAADL-----STAQAIELANAMRAKGPAVVVITRGAQGALAVDSQGVHERAAR 213

Query: 240 PVASVDTTGAGDAFVAGLLASLAA 263
           P A VD+ GAGD F+A  L +  A
Sbjct: 214 PCAFVDSMGAGDGFIAAFLLAWQA 237


Lambda     K      H
   0.320    0.133    0.392 

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: 201
Number of extensions: 12
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 307
Length of database: 284
Length adjustment: 26
Effective length of query: 281
Effective length of database: 258
Effective search space:    72498
Effective search space used:    72498
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 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