GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Klebsiella michiganensis M5al

Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate BWI76_RS27555 BWI76_RS27555 putative sugar kinase/transcriptional regulator, ATPase domain protein

Query= SwissProt::P23917
         (302 letters)



>FitnessBrowser__Koxy:BWI76_RS27555
          Length = 310

 Score =  229 bits (585), Expect = 5e-65
 Identities = 123/296 (41%), Positives = 171/296 (57%), Gaps = 2/296 (0%)

Query: 3   IGIDLGGTKTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAEQATGQRGTVGM 62
           +G+D+GG+K   + + + G +  R R+ T +   +Q I T+  L+        Q   +G+
Sbjct: 4   LGLDIGGSKIAAVVMDEQGHEWRRFRVETRKQTRQQFIATLVELITAIGDELAQPLAIGI 63

Query: 63  GIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDGAAAGA 122
            +PGSISP +G ++NAN   +NG     +L  RL + V LAND NC A+SEA DGA A  
Sbjct: 64  ALPGSISPQSGKIRNANIQVINGCRLQDELEQRLGQSVVLANDGNCFALSEACDGAGADY 123

Query: 123 QTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDELRYREEVPCYCGKQG 182
             VF + +GTGCG G+A N +   G +G A E GH  LP     E+       CYCGK  
Sbjct: 124 SLVFGMTLGTGCGGGIALNRQIFPGASGIAAECGHITLP--GYQEVNDGPPARCYCGKYN 181

Query: 183 CIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYELRLAKSLAHVVNI 242
           C+E+FISGTG +  YR L+  AL    II    E +  A   + R+  +LA++LA VVN+
Sbjct: 182 CVESFISGTGLSARYRLLTQEALSSQAIIARALEGEHAACEQVLRFRQQLARTLATVVNL 241

Query: 243 LDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRKAKHGDSSGVRGAAWL 298
           +DP VI+LGGG+SNV  L   +   +   VF     TP+  A+HGDSSG+RGAAWL
Sbjct: 242 IDPGVIILGGGLSNVALLVNDLEADVAPLVFTDHFITPIVPARHGDSSGMRGAAWL 297


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: 313
Number of extensions: 10
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: 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.

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