GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Dyella japonica UNC79MFTsu3.2

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate N515DRAFT_1253 N515DRAFT_1253 2-dehydro-3-deoxy-L-fuconate dehydrogenase (EC 1.1.1.-)

Query= reanno::pseudo5_N2C3_1:AO356_20240
         (272 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1253
          Length = 248

 Score =  145 bits (365), Expect = 1e-39
 Identities = 91/252 (36%), Positives = 138/252 (54%), Gaps = 10/252 (3%)

Query: 18  RLKDKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAQKVEAVAAHWRERGADVHALQA 77
           RL  K  L+T A  GIG A   AFA + AR++ +DI  Q + A++A       ++   + 
Sbjct: 4   RLAGKHALVTAAGAGIGRATALAFAREGARVLATDIDEQALAALSAE----APELRTERL 59

Query: 78  DVSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGC 137
           DV+    +     R V  H   DVL NCAG       L+  +  W+R FAI++D  ++ C
Sbjct: 60  DVTDPVQID----RLVASHPPFDVLFNCAGYVHAGTILDTDDAAWKRSFAINVDSMFHLC 115

Query: 138 KAVLPQMIEQGVGSIINIASVHSS-HIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVN 196
           + VLP M+E+G GSI+N++SV SS   +P  F Y   K  ++GLT+++  ++  +G+R N
Sbjct: 116 QRVLPAMLERGGGSIVNMSSVASSIKGVPNRFAYSTTKAAVIGLTKSVAADFVGRGIRCN 175

Query: 197 AIAPGYIETQLNVDYWNGF-ADPHAERQRALDLHPPRRVGQPIEVAMTAVFLASDEAPFI 255
           AI PG ++T    D       D  A  +  ++  P  R+G P E+AM A++LASDEA F 
Sbjct: 176 AICPGTVKTPSLGDRVRALGGDEDAVWRGFVERQPMGRLGNPEEIAMLALYLASDEAAFT 235

Query: 256 NASCITIDGGRS 267
             +   +DGG S
Sbjct: 236 TGTVHIVDGGWS 247


Lambda     K      H
   0.321    0.137    0.419 

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: 163
Number of extensions: 7
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: 272
Length of database: 248
Length adjustment: 24
Effective length of query: 248
Effective length of database: 224
Effective search space:    55552
Effective search space used:    55552
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.

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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