GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsK in Burkholderia phytofirmans PsJN

Align ribokinase (EC 2.7.1.15) (characterized)
to candidate BPHYT_RS09175 BPHYT_RS09175 2-dehydro-3-deoxygluconokinase

Query= BRENDA::A0A0H2UL04
         (309 letters)



>FitnessBrowser__BFirm:BPHYT_RS09175
          Length = 312

 Score =  106 bits (265), Expect = 6e-28
 Identities = 86/287 (29%), Positives = 138/287 (48%), Gaps = 21/287 (7%)

Query: 35  NYQVIPGGKGANQAVAAARMQADVGFIACVGDDSFGINIRESFKLDGINTAGVKLQPNCP 94
           NY    GG  +N  +AAAR  A  GF++ VG D FG  + + ++ + ++T+ V++ P   
Sbjct: 31  NYLQGFGGDTSNFCIAAARQGAQTGFVSAVGADHFGRLLVDLWEREQVDTSLVRVDPQAS 90

Query: 95  TGIAMIQVSDSGENSICISAEANAKLTAAAIEPDLAAIRDARYL------LMQLETPLDG 148
           TG+  +    +G     + A + A   A    P L AI  A+ +      L    +  D 
Sbjct: 91  TGVYFVSHGPNGHAFDYLRAGSAASRYAPHDLP-LDAIAAAKVIHLSGISLAISLSACDA 149

Query: 149 ILKAAQEAK------TAKTNVILNPAP---ARELPDELLKCVDLITPNETEAEVLTGITV 199
            L+A   A+      +  TN+ L   P   AR +  E ++  D+  P+  +   LTG+T 
Sbjct: 150 ALEAIAHARANGVRVSFDTNLRLKLWPLARARAVMLEAIRQTDICLPSWDDVTDLTGLTG 209

Query: 200 YDDSSAQQAADALHCKGIEIVIITLGSKGVWLSQNGRGQRIPGFVVKATDTTAAGDTFNG 259
            D+       D L   G  +V + LG +G +++     + +PG VV A D T AGD F G
Sbjct: 210 RDE-----IVDFLLSHGPSVVALKLGKEGSYIATPNERRVVPGHVVNAVDATGAGDCFGG 264

Query: 260 ALVTGLLQEMPLESAIKFAHAAAAISVTRFGAQTSIPTRAEVEAFLA 306
           A +  ++      +A ++A+ AAA+S   +GA   IP+RA VE  LA
Sbjct: 265 AFIARIVAGDDPFTAARYANVAAALSTQGYGAVAPIPSRATVEQLLA 311


Lambda     K      H
   0.316    0.132    0.373 

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: 191
Number of extensions: 5
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: 309
Length of database: 312
Length adjustment: 27
Effective length of query: 282
Effective length of database: 285
Effective search space:    80370
Effective search space used:    80370
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