GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsK in Escherichia coli BW25113

Align Ribokinase; RK; EC 2.7.1.15 (uncharacterized)
to candidate 17923 b3883 putative kinase (VIMSS)

Query= curated2:Q9K6K1
         (294 letters)



>FitnessBrowser__Keio:17923
          Length = 298

 Score =  115 bits (288), Expect = 1e-30
 Identities = 96/295 (32%), Positives = 141/295 (47%), Gaps = 15/295 (5%)

Query: 6   ITVVGSINMDMVTITDVVPVQGETVLGKDFRTVPGGKGANQAVAAARLGANVRMIGRVGD 65
           +  VG   MD +   + +P +    + +++  V GG  A  AVAAARLGA V  IGRVGD
Sbjct: 4   VACVGITVMDRIYYVEGLPTESGKYVARNYTEVGGGPAATAAVAAARLGAQVDFIGRVGD 63

Query: 66  DPFGHVLTENLAKEGIITDSVKPVTDCTSGVATILLSDRDNRIIVTKGANEHVTPDYVAA 125
           D  G+ L   L   G+ T   K      S  + I++  +  RII+   + + + PD    
Sbjct: 64  DDTGNSLLAELESWGVNTRYTKRYNQAKSSQSAIMVDTKGERIIINYPSPD-LLPDAEWL 122

Query: 126 FEQELAASDVVLLQLEIPLETVAYVLEFCAKHHVTTVLNP--APAQKLPDAAWTDATYIS 183
            E + +  DVVL  +    +          +  V TVL+    P       A +D    S
Sbjct: 123 EEIDFSQWDVVLADVRWH-DGAKKAFTLARQAGVMTVLDGDITPQDISELVALSDHAAFS 181

Query: 184 PNENECLQLFG-DEPDANLRQ-------KLIMTKGADGVQFYENDEQVQVESFRVEPVDT 235
             E    +L G  E  + L+Q        + +T+G+ G  + EN  +    +F+V+ VDT
Sbjct: 182 --EPGLARLTGVKEMASALKQAQTLTNGHVYVTQGSAGCDWLENGGRQHQPAFKVDVVDT 239

Query: 236 TGAGDTFNGAFAVALG-GGTVKEAVRFANAAAALSVQSFGAQGGMPTKAQVQSFL 289
           TGAGD F+GA AVAL   G + E+VRFA+  AAL     G + G+P   Q +SFL
Sbjct: 240 TGAGDVFHGALAVALATSGDLAESVRFASGVAALKCTRPGGRAGIPDCDQTRSFL 294


Lambda     K      H
   0.315    0.132    0.377 

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: 228
Number of extensions: 10
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: 294
Length of database: 298
Length adjustment: 26
Effective length of query: 268
Effective length of database: 272
Effective search space:    72896
Effective search space used:    72896
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 (21.6 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