GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Klebsiella michiganensis M5al

Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate BWI76_RS16755 BWI76_RS16755 acetoin reductase

Query= reanno::Korea:Ga0059261_1894
         (259 letters)



>FitnessBrowser__Koxy:BWI76_RS16755
          Length = 256

 Score =  134 bits (338), Expect = 1e-36
 Identities = 88/250 (35%), Positives = 129/250 (51%), Gaps = 11/250 (4%)

Query: 19  KRVLVTGGGSGIGAGIVEGFARQGADVTFFDIAGAESQLLVERLSADGHKACFERVDLTD 78
           K  LVTG G GIG  I     + G  V   D   A +Q + + ++  G +A   +VD++ 
Sbjct: 3   KVALVTGAGQGIGKAIALRLVKDGFAVAIADYNDATAQAVADEINRSGGRALAVKVDVSQ 62

Query: 79  VASLQAVIARLIKGAGGFDILVNNAANDDRHAIDEITEAYWDERLSVNLKHIFFCAQAVV 138
              + A + +  KG GGFD++VNNA       I+EI E   D+  ++N+K + +  QA V
Sbjct: 63  RDQVFAAVEQARKGLGGFDVIVNNAGVAPSTPIEEIREDVIDKVYNINVKGVIWGIQAAV 122

Query: 139 PAMRARG-GGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLGRDGIRATCVIP 197
            A +  G GG I+N  S + H+G  +L +Y + K A+ GLT++ ARDL   GI      P
Sbjct: 123 EAFKQEGHGGKIINACSQAGHVGNPELAVYSSSKFAVRGLTQTAARDLAHLGITVNGYCP 182

Query: 198 GNVRTPRQLKWYSPEGEA---------EIVAAQCLDGRLA-PEDVAAMVLFLASDDARLV 247
           G V+TP   +      EA         +  A +   GRL+ PEDVAA V +LA  D+  +
Sbjct: 183 GIVKTPMWAEIDRQVSEAAGKPLGYGTQEFAKRITLGRLSEPEDVAACVSYLAGPDSNYM 242

Query: 248 TGHSYFVDAG 257
           TG S  +D G
Sbjct: 243 TGQSLLIDGG 252


Lambda     K      H
   0.321    0.137    0.409 

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: 160
Number of extensions: 5
Number of successful extensions: 3
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: 259
Length of database: 256
Length adjustment: 24
Effective length of query: 235
Effective length of database: 232
Effective search space:    54520
Effective search space used:    54520
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 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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