GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagK in Klebsiella michiganensis M5al

Align N-acetyl-D-glucosamine kinase; EC 2.7.1.59; GlcNAc kinase (uncharacterized)
to candidate BWI76_RS27555 BWI76_RS27555 putative sugar kinase/transcriptional regulator, ATPase domain protein

Query= curated2:Q4QP08
         (304 letters)



>FitnessBrowser__Koxy:BWI76_RS27555
          Length = 310

 Score =  191 bits (486), Expect = 1e-53
 Identities = 109/300 (36%), Positives = 165/300 (55%), Gaps = 6/300 (2%)

Query: 2   YYGLDIGGTKIELAVFNEELEKLYSERVPTPKTDYEEWLNTIVDLVNRADEKFGEVGTVG 61
           Y GLDIGG+KI   V +E+  +    RV T K   ++++ T+V+L+    ++  +   +G
Sbjct: 3   YLGLDIGGSKIAAVVMDEQGHEWRRFRVETRKQTRQQFIATLVELITAIGDELAQPLAIG 62

Query: 62  LGVPGFVNQQTGLAEITNIRVADNKPILRDLSVRLGREVRAENDANCFALSEAWDTENQQ 121
           + +PG ++ Q+G     NI+V +   +  +L  RLG+ V   ND NCFALSEA D     
Sbjct: 63  IALPGSISPQSGKIRNANIQVINGCRLQDELEQRLGQSVVLANDGNCFALSEACDGAGAD 122

Query: 122 YPTVLGLILGTGFGGGFVLNGKVHSGQVGMAGELGHLQL-NYHALKLLGWDNAPIYQCGC 180
           Y  V G+ LGTG GGG  LN ++  G  G+A E GH+ L  Y  +     ++ P  +C C
Sbjct: 123 YSLVFGMTLGTGCGGGIALNRQIFPGASGIAAECGHITLPGYQEV-----NDGPPARCYC 177

Query: 181 GNKACLDNYLSGRGFEMLYRDLKGETLSAREIIDLFYQGNESAVDFVNLFVELAAISIGN 240
           G   C+++++SG G    YR L  E LS++ II    +G  +A + V  F +  A ++  
Sbjct: 178 GKYNCVESFISGTGLSARYRLLTQEALSSQAIIARALEGEHAACEQVLRFRQQLARTLAT 237

Query: 241 IITAFDPHMIVLGGGLSNFDYLYEALPKALPPHLMRTAKVPPIKKAKHGDSGGVRGAAAL 300
           ++   DP +I+LGGGLSN   L   L   + P +     + PI  A+HGDS G+RGAA L
Sbjct: 238 VVNLIDPGVIILGGGLSNVALLVNDLEADVAPLVFTDHFITPIVPARHGDSSGMRGAAWL 297


Lambda     K      H
   0.319    0.140    0.421 

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: 227
Number of extensions: 9
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: 304
Length of database: 310
Length adjustment: 27
Effective length of query: 277
Effective length of database: 283
Effective search space:    78391
Effective search space used:    78391
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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