GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Shewanella sp. ANA-3

Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate 7026976 Shewana3_4105 L-threonine 3-dehydrogenase (RefSeq)

Query= CharProtDB::CH_000596
         (353 letters)



>FitnessBrowser__ANA3:7026976
          Length = 341

 Score =  191 bits (485), Expect = 2e-53
 Identities = 103/314 (32%), Positives = 172/314 (54%), Gaps = 9/314 (2%)

Query: 26  PVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFILGHECAGEIAAVGSSVDQ 85
           P P++ H+++LIK+    ICG+D+H Y         +  P ++GHE  GE+  +G  V  
Sbjct: 19  PKPEMGHNDLLIKIKKTAICGTDMHIYNWDEWSQKTIPVPMVVGHEYVGEVVDIGQEVRG 78

Query: 86  FKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLATPPVDGAFVQYIKMRQDFVFLIPD 145
           FK+GDRV+ E  +TCG C  C+ GR +LC +   +     +G+F +Y+ +     F IPD
Sbjct: 79  FKIGDRVSGEGHITCGHCRNCRAGRTHLCRNTSGVGVNR-EGSFAEYLVIPAFNAFKIPD 137

Query: 146 SLSYEEAALIEPFSVGIHAAARTKLQPGSTIAIMGMGPVGLMAVAAAKAFGAGTIIVTDL 205
            +S + A++ +PF   +H A    L  G  + I G GP+G+MA A  +  GA  +++TD+
Sbjct: 138 DISDDLASIFDPFGNAVHTALSFDL-VGEDVLITGAGPIGIMAAAVCRHVGARHVVITDV 196

Query: 206 EPLRLEAAKKMGATHIINIREQDALEEIKTITNDRGVDVAWETAGNPAALQSALASVRRG 265
              RLE A+KMGAT  +N+ ++   + +K +    G DV  E +G P+A  + L ++  G
Sbjct: 197 NEYRLELARKMGATRAVNVAQESLKDVMKELGMTEGFDVGLEMSGVPSAFHAMLDTMNHG 256

Query: 266 GKLAIVGLPSQNEIPLNVPFIADNEIDIYGIF--RYANTYPKGIEFLASGIVDTKHLVTD 323
           GK+A++G+P   E+ ++   +    + I GI+      T+ K    + SG+ D   ++T 
Sbjct: 257 GKIAMLGIPG-GEMAIDWSKVIFKGLVIKGIYGREMFETWYKMASLIQSGL-DISPIITH 314

Query: 324 QYSLEQTQ---DAM 334
            Y ++  Q   DAM
Sbjct: 315 HYKIDDFQKGFDAM 328


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: 284
Number of extensions: 13
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: 353
Length of database: 341
Length adjustment: 29
Effective length of query: 324
Effective length of database: 312
Effective search space:   101088
Effective search space used:   101088
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