GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Halococcus hamelinensis 100A6

Align fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_049904537.1 C447_RS14190 sugar kinase

Query= BRENDA::Q6VWJ5
         (386 letters)



>NCBI__GCF_000336675.1:WP_049904537.1
          Length = 318

 Score =  143 bits (360), Expect = 8e-39
 Identities = 100/313 (31%), Positives = 158/313 (50%), Gaps = 12/313 (3%)

Query: 65  SSLVVCFGEMLIDFVPTTSGLSLAEAPAFKKAPGGAPANVAVGISRLGGSSAFIGKVGED 124
           SS VV  GE ++   P+T+G  +  A  F+K+  GA  NVA+G++RLG    +  K+G D
Sbjct: 2   SSRVVTLGETMVLVYPSTTG-PMKHAHEFEKSLAGAETNVAIGLARLGHDVGWYSKLGTD 60

Query: 125 EFGYMLAEILKENNVNSDGMRFDPGARTALAFVTLRKDGEREFMFYRNPSADMLLQEDEL 184
             G  L   ++   V++  + F   A T + F   R+ GE    +YR+ SA  L+  D+L
Sbjct: 61  PHGEYLEFFVRGEGVDTTTVEFTDEAPTGIMFKERREFGEPAVHYYRHGSAASLMSPDDL 120

Query: 185 DLELIRKAKVFHYGSIS-LITEPCKSAHIAAAKAAKDAGVILSYDPNLRLPLWPSAESAR 243
            ++ +  A+  H   I+  ++E C+ A + AA+ A +AG+ +S+DPN+R  LW S E  R
Sbjct: 121 PVDYLTNAEYLHLTGITPALSESCRDATLLAAERATEAGMTVSFDPNVRRKLWESDERMR 180

Query: 244 EGILSIWNTADIIKISEEEISFLTQGEDPYDDNVVRKLYHPNLKLLLVTEGPEGCRYYTK 303
           E +L + + +DI+    EE + L   +DP  + +            +V  G  G      
Sbjct: 181 ETMLDLVSLSDIVLPGIEEGAALFGTDDP--EAIAAACLDHGAGTAVVKLGAAGAVVADG 238

Query: 304 DFSGRVKGIKVD-AVDTTGAGDAFVAGILSQLASDVSLLQDEGKLRDALSFANACGALTV 362
             + RV G  V+  VD  GAGD F AG L+      S ++ +G + +A   ANA GA   
Sbjct: 239 STTERVSGYDVERVVDPVGAGDGFAAGFLA------SRIEGQGPV-EATETANAVGAFAT 291

Query: 363 MERGAIPALPTKE 375
              G    LPT++
Sbjct: 292 TVAGDTEGLPTRK 304


Lambda     K      H
   0.317    0.134    0.382 

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: 230
Number of extensions: 12
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: 386
Length of database: 318
Length adjustment: 29
Effective length of query: 357
Effective length of database: 289
Effective search space:   103173
Effective search space used:   103173
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: 49 (23.5 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