GapMind for catabolism of small carbon sources

 

Aligments for a candidate for scrK in Shewanella amazonensis SB2B

Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate 6937235 Sama_1405 fructokinase (RefSeq)

Query= SwissProt::P23917
         (302 letters)



>lcl|FitnessBrowser__SB2B:6937235 Sama_1405 fructokinase (RefSeq)
          Length = 310

 Score =  367 bits (942), Expect = e-106
 Identities = 175/298 (58%), Positives = 218/298 (73%), Gaps = 4/298 (1%)

Query: 2   RIGIDLGGTKTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAEQATGQRGTVG 61
           R GIDLGGTK E++ L + GE+++R R+PTP+D YR T+E +A LV  +E+ TGQ  +VG
Sbjct: 3   RSGIDLGGTKIELVTLNEKGEEVFRKRVPTPKD-YRATLEAVAGLVHDSEKETGQVSSVG 61

Query: 62  MGIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDGAAAG 121
           +GIPG +S  TG VKN+N+ WLNGQP DKDL A L REVR+ANDANC AVSE+VDG  AG
Sbjct: 62  IGIPGVVSAVTGRVKNSNAVWLNGQPMDKDLGAMLGREVRIANDANCFAVSESVDGGGAG 121

Query: 122 AQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDELRYREEVPCYCGKQ 181
              VF  I+GTGCGAG+A N + H GGNG  GEWGHNPLPWM  DE        C+CG  
Sbjct: 122 KTLVFGAILGTGCGAGIAINHKVHGGGNGIGGEWGHNPLPWMTADEF---NSTRCFCGNA 178

Query: 182 GCIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYELRLAKSLAHVVN 241
            CIETF+SGTGF  D+R   G A  G EI+ L+ + +P+AE A  R+  RLA++LAHV+N
Sbjct: 179 DCIETFVSGTGFVRDFRAHGGEAASGIEIVALMGKGEPLAEAAFGRFIDRLARALAHVIN 238

Query: 242 ILDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRKAKHGDSSGVRGAAWLW 299
           +LDPDVIVLGGG+SN+D +Y+ +  L+ ++V GGEC T V K  HG SSGVRGAAWLW
Sbjct: 239 LLDPDVIVLGGGVSNIDEIYEYLPALLPKYVLGGECATKVVKNHHGASSGVRGAAWLW 296


Lambda     K      H
   0.318    0.137    0.418 

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: 395
Number of extensions: 21
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: 302
Length of database: 310
Length adjustment: 27
Effective length of query: 275
Effective length of database: 283
Effective search space:    77825
Effective search space used:    77825
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 (21.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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