GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Bacteroides clarus YIT 12056

Align fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_009122457.1 BUB52_RS02800 carbohydrate kinase

Query= BRENDA::C4M2I2
         (294 letters)



>NCBI__GCF_900129655.1:WP_009122457.1
          Length = 294

 Score =  233 bits (595), Expect = 3e-66
 Identities = 128/286 (44%), Positives = 179/286 (62%), Gaps = 4/286 (1%)

Query: 8   VAGIGEVVWDCFGDVKKQGGAPCNFAMHMAQFGFESYAFIAVGNDELGKRSLEIIHSFGV 67
           V G+GE +WDC  + KK GGAP NFA H++QFGF+S    AVG D  G   LE+    G+
Sbjct: 5   VVGMGEALWDCLPEGKKIGGAPANFAYHVSQFGFDSRVVSAVGADADGDEILEVFAQKGL 64

Query: 68  QTIDPVVDYETSTVIITLHN-GIPSYNVKLNVAWDHLKLTDSIIEKAKELDAVCFGTIAQ 126
           +T    V Y T TV +TL   G+P Y +K  VAWD++  TD +   A    AVCFG++AQ
Sbjct: 65  RTQIERVPYPTGTVQVTLDAMGVPCYEIKEGVAWDNIPFTDELKRLALNTRAVCFGSLAQ 124

Query: 127 RSEETRKSIIQFLKLMKP--NSFKVFDVNLRQHFYNDDIIQESLSLSNIVKMSDEEIQEV 184
           R+E +R +I +FL  M       K+FD+NLRQ FY  +I+ +S+   N++K++DEE+  +
Sbjct: 125 RNEVSRITINRFLDTMPDCEEQLKIFDINLRQGFYTKEILCDSMRRCNVLKINDEELVTI 184

Query: 185 GKACGFQGNDLEILKQIH-HQYHLKYSLLTLGEKGSYVYDGTNEIFCEPTKVNVVNTVGA 243
            +  G+ G DL+    I   +Y+LK  +LT G  GSYV+      F E  +V V +TVGA
Sbjct: 185 SRIFGYPGIDLQDKCWILLAKYNLKMLILTCGTNGSYVFTPGVVSFQETPRVPVADTVGA 244

Query: 244 GDSFTAIFVGSILKGKSIEQAQKLASKVASYVCTQDSAMPKLTQEL 289
           GDSFTA F  ++L GK +++A KLA +V++YVCTQ  AMP+L Q L
Sbjct: 245 GDSFTAAFTSAVLSGKPVQEAHKLAVEVSAYVCTQSGAMPELPQVL 290


Lambda     K      H
   0.318    0.135    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: 241
Number of extensions: 8
Number of successful extensions: 4
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: 294
Length adjustment: 26
Effective length of query: 268
Effective length of database: 268
Effective search space:    71824
Effective search space used:    71824
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: 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