GapMind for catabolism of small carbon sources

 

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

Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate N515DRAFT_0039 N515DRAFT_0039 L-threonine 3-dehydrogenase

Query= CharProtDB::CH_000596
         (353 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0039
          Length = 344

 Score =  183 bits (465), Expect = 5e-51
 Identities = 113/347 (32%), Positives = 179/347 (51%), Gaps = 10/347 (2%)

Query: 5   VPQNMKAAVMHNTRE-IKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVE 63
           +PQ MKA V     + I +E +PVP++  +EVLIK+    ICG+DLH Y         ++
Sbjct: 1   MPQTMKALVKRLPEQGIWMEEVPVPEVGPNEVLIKMEKTAICGTDLHIYKWDEWSQRTIK 60

Query: 64  KPFILGHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLATP 123
               +GHE  G I  +G  V  +KVGDRV+ E  + CG C  C+ GR +LCP+   +   
Sbjct: 61  PGLTIGHEFVGRIVDIGPGVTGYKVGDRVSAEGHIVCGHCRNCRAGRQHLCPNTVGIGVN 120

Query: 124 PVDGAFVQYIKMRQDFVFLIPDSLSYEEAALIEPFSVGIHAAARTKLQPGSTIAIMGMGP 183
             +GAF +Y+ M    ++ IPD +  E AA  +P+    H A    L  G  + I G GP
Sbjct: 121 R-NGAFAEYMTMPASNLWPIPDQIPSELAAFFDPYGNAAHCALEFDL-IGEDVLITGAGP 178

Query: 184 VGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKTITNDRGVD 243
           +G++A   AK  GA  ++VTD+   RL+ A  MGAT ++N+  Q   + +K + +  G D
Sbjct: 179 IGIIAAGIAKHVGARNVVVTDVNDYRLKLAADMGATRVVNVANQSLRDVVKDL-HIEGFD 237

Query: 244 VAWETAGNPAALQSALASVRRGGKLAIVGLPSQNEIPLNVPFIADNEIDIYGIF--RYAN 301
           V  E +GNP A    L  +  GGK+A++G+  +    ++   +    + + GI+  R   
Sbjct: 238 VGLEMSGNPRAFNDMLDCMYHGGKIALLGIMPRG-AGIDWDKVIFKGLTLQGIYGRRMYE 296

Query: 302 TYPKGIEFLASGIVDTKHLVTDQYSLEQTQDAMERALQFKNECLKVM 348
           T+ K  + + SG    + ++T Q  ++  Q   +  L     C KV+
Sbjct: 297 TWYKMTQMVLSGF-PLQKVLTHQIHIDDFQKGFD--LMDAGHCGKVV 340


Lambda     K      H
   0.320    0.137    0.401 

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: 286
Number of extensions: 15
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: 353
Length of database: 344
Length adjustment: 29
Effective length of query: 324
Effective length of database: 315
Effective search space:   102060
Effective search space used:   102060
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 (21.8 bits)
S2: 49 (23.5 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