GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Kocuria flava HO-9041

Align Fructokinase-1; Fructokinase I; OsFKI; EC 2.7.1.4 (characterized)
to candidate WP_058858206.1 AS188_RS06715 5-dehydro-2-deoxygluconokinase

Query= SwissProt::A2WXV8
         (323 letters)



>NCBI__GCF_001482365.1:WP_058858206.1
          Length = 328

 Score =  129 bits (324), Expect = 1e-34
 Identities = 97/321 (30%), Positives = 149/321 (46%), Gaps = 18/321 (5%)

Query: 8   VVSFGEMLIDFVPTVAGVSLAEAPAFVKAPGGAPANVAIAVARLGGGAAFVGKLGDDEFG 67
           VV+ G + +D  P   G+ L +  +F K  GG+PANVA+A AR G  AA + + G+D FG
Sbjct: 5   VVTMGRISVDIYPNEIGMGLEDVTSFGKYLGGSPANVAVAAARHGESAALISRTGEDPFG 64

Query: 68  RMLAAILRDNGVDDGGVVFDAGARTALAFVTLRADGEREFMFY-RNPSA-DMLLTHAELN 125
             L   L   GVDD  V    G +T   F  +    +    FY R P+A D+ +   E++
Sbjct: 65  TYLHRELVRYGVDDTFVTPVPGLQTPATFCAIMPPEDFPLYFYGRFPTAPDLQIRPEEID 124

Query: 126 VELIKRAAVFHYGSISLIAEPCRSAHLRA------MEIAKEAGALLSYDPNLREALWPSR 179
              ++ A +       L  EP RSA L A       ++  +   +L  D   R   W S 
Sbjct: 125 TATVRDARILWSTVTGLCQEPSRSAQLAAHTARPREQLRPDQHTVLDLD--YRPMFWASE 182

Query: 180 EEARTKILSIWDHADIVKVSEVELEFLTGIDSVEDDVVMKLWRPTMKLLLVTLGDQGCKY 239
           EEAR ++  +  H  I   ++ E     G +   D+   +L    +++ +V LG +G   
Sbjct: 183 EEAREQVHELLRHVSIAIGNDKECAVAVG-EGTPDEQADRLLEAGVRIAVVKLGPEGVMA 241

Query: 240 YARDFRGAVPSYKVQQVDTTGAGDAFVGALLRRIVQDPSSLQDQKKLEEAIKFANACGAI 299
             R+ R       V+ V+  GAGD+F GA           L     LE+ + +ANA GAI
Sbjct: 242 KTREERVVSAPVPVETVNGLGAGDSFGGAFCH-------GLNQGWPLEQVLDYANAAGAI 294

Query: 300 TATKKGAIPSLPTEVEVLKLM 320
            A++     ++PT  EV +L+
Sbjct: 295 VASRISCSDAMPTPDEVFQLL 315


Lambda     K      H
   0.320    0.136    0.389 

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: 251
Number of extensions: 21
Number of successful extensions: 5
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: 323
Length of database: 328
Length adjustment: 28
Effective length of query: 295
Effective length of database: 300
Effective search space:    88500
Effective search space used:    88500
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 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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