GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Klebsiella michiganensis M5al

Align Fructokinase; EC 2.7.1.4 (uncharacterized)
to candidate BWI76_RS27485 BWI76_RS27485 aminoimidazole riboside kinase

Query= curated2:P22824
         (307 letters)



>FitnessBrowser__Koxy:BWI76_RS27485
          Length = 319

 Score =  248 bits (633), Expect = 1e-70
 Identities = 125/305 (40%), Positives = 184/305 (60%), Gaps = 1/305 (0%)

Query: 1   MNQVWVTGDAVVDLIPESETSLLKCPGGAPANVAVAIARLSGKSAFFGRVGDDPFGRFMQ 60
           MN+VW  GDA VDL+PE + S LKCPGGA ANV V +ARL G   F G +GDD  GRF++
Sbjct: 4   MNKVWAIGDASVDLVPEKQNSYLKCPGGASANVGVCVARLGGTCGFIGCLGDDDAGRFLR 63

Query: 61  SILDQEGVCTEFLIKDPEQRTSTVVVDLDDQGERSFTFMVKPSADQFMSVEDMGNFKQGD 120
            +    GV    L  D    ++ ++V+L   GERSFT++V P AD ++S +D+  F++ +
Sbjct: 64  QVFQDNGVDVSSLRLDASLTSAVLIVNLTADGERSFTYLVHPGADTYVSPQDLPTFRKYE 123

Query: 121 WLHVCSISLANEPSRSSTFEAIKRAKAAGGFISFDPNLRDEVWQDQSEIQAVVMKAVAMA 180
           W +  SI L + P+R +  E  +R + AGG++ FD NLR ++W++ +EI  ++ ++ A+A
Sbjct: 124 WFYFSSIGLTDSPAREACLEGARRMREAGGYVLFDVNLRSKMWRNTAEIPDLIARSAALA 183

Query: 181 DVVKFSEEELLFLTDSTSMAQGLQQIAAMNIALVLVTQGAKGVWRVFESQSELITGQVVS 240
            + K S +EL  L+ ++        +  +     +++ GA+G   +      L     V 
Sbjct: 184 SICKVSADELCQLSGASHWQDARYYMRDLGCDTTIISLGAEGALLITAEGEFLFPAPRVE 243

Query: 241 PIDTTGAGDAFVGGLLACLSRHADWKNHPVVSSAIQWANGCGALATTQKGAMTALPTQTE 300
            +DTTGAGDAFVGGLL  LSR   W NH +++ AI  AN CGA+A T KGAMTALP   +
Sbjct: 244 VVDTTGAGDAFVGGLLFTLSRENYW-NHALLAEAISNANACGAMAVTAKGAMTALPYPDQ 302

Query: 301 LLRFI 305
           L  F+
Sbjct: 303 LNTFL 307


Lambda     K      H
   0.318    0.132    0.388 

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: 255
Number of extensions: 7
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: 307
Length of database: 319
Length adjustment: 27
Effective length of query: 280
Effective length of database: 292
Effective search space:    81760
Effective search space used:    81760
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 (21.8 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