GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Sinorhizobium meliloti 1021

Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate SMc03109 SMc03109 hypothetical protein

Query= SwissProt::P23917
         (302 letters)



>FitnessBrowser__Smeli:SMc03109
          Length = 298

 Score =  321 bits (823), Expect = 1e-92
 Identities = 163/299 (54%), Positives = 200/299 (66%), Gaps = 3/299 (1%)

Query: 1   MRIGIDLGGTKTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAEQATGQRGTV 60
           M IGID GGTK EVIAL   GE   RHR+PTP   Y   I  +  LV  AE   G+RG++
Sbjct: 1   MFIGIDWGGTKMEVIALDRDGETRARHRVPTPTSGYEDCIRAVVELVASAESTAGERGSI 60

Query: 61  GMGIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDGAAA 120
           G+GIPGS +P TG+V+N+N+  +NG+P  +DL+A L REVRLANDANCLAVSEAVDGA  
Sbjct: 61  GIGIPGSPNPRTGIVRNSNAVLINGKPLGRDLAAALGREVRLANDANCLAVSEAVDGAGK 120

Query: 121 GAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDELRYREEVPCYCGK 180
            A  VF VI+GTG G G+A   + H G  G A E GH PLPWM +DE        C+CGK
Sbjct: 121 DAGVVFGVIVGTGHGGGLAIGKKVHAGYQGVAAEIGHYPLPWMTKDEYPGHR---CWCGK 177

Query: 181 QGCIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYELRLAKSLAHVV 240
            GC++ +  GTG  +DYR  +G   +G +II      DPVA     R+  RLA+SLA + 
Sbjct: 178 LGCLDMYACGTGLELDYRMTTGTDRRGRDIIEAKRAGDPVAIGVYGRFVDRLARSLALLT 237

Query: 241 NILDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRKAKHGDSSGVRGAAWLW 299
           NI+DPDV VLGGGMSNVD +Y  +   I +++FG   ETP+RKA HGDSSGVRGAAWLW
Sbjct: 238 NIVDPDVFVLGGGMSNVDEIYGELPASITRYLFGDSFETPIRKAVHGDSSGVRGAAWLW 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: 336
Number of extensions: 12
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: 302
Length of database: 298
Length adjustment: 27
Effective length of query: 275
Effective length of database: 271
Effective search space:    74525
Effective search space used:    74525
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 (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