GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Pandoraea thiooxydans ATSB16

Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate WP_047213848.1 PATSB16_RS09090 zinc-dependent alcohol dehydrogenase family protein

Query= CharProtDB::CH_000596
         (353 letters)



>NCBI__GCF_001931675.1:WP_047213848.1
          Length = 345

 Score =  151 bits (381), Expect = 3e-41
 Identities = 105/352 (29%), Positives = 176/352 (50%), Gaps = 16/352 (4%)

Query: 9   MKAAVMHNTREIKIETLPVPDINH-DEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFI 67
           MKA +     E+ +E  P P++    + ++KV    ICG+DLH    G +      +  I
Sbjct: 1   MKALIYRGPGELALEERPHPELYAATDAIVKVTKTTICGTDLHIL-KGDVPTCAPGR--I 57

Query: 68  LGHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLATPPVDG 127
           LGHE  G +  VG+ V  F  GD V +    +CG+C AC++G Y+ C    ++    +DG
Sbjct: 58  LGHEGVGIVEQVGTGVTAFMPGDPVLISCISSCGKCAACRKGMYSHCETGGWILGNRIDG 117

Query: 128 AFVQYIKM--RQDFVFLIPDSLSYEEAALIEP-----FSVGIHAAARTKLQPGSTIAIMG 180
              +Y+++      ++ IP +   E   ++       F  G+      K+QPG+T+AI+G
Sbjct: 118 TQAEYVRIPHADTSLYRIPPNADEEALVMLSDILPTGFECGV---LNGKVQPGNTVAIVG 174

Query: 181 MGPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKTITNDR 240
            GP+GL A+  A+ +    +IV D +  RLE A++ GA+  I+  + D L+EI+ +T   
Sbjct: 175 AGPIGLAALLTAQFYSPAQLIVIDRDTSRLEVARRFGASATIDPDQTDPLKEIQRLTGGA 234

Query: 241 GVDVAWETAGNPAALQSALASVRRGGKLAIVGLPSQNEIPLNVPFIADNEIDIYGIFRYA 300
           GVD A E  G PA  Q     V  GG +A VG+    +  L++  + D  I I       
Sbjct: 235 GVDTAIEAVGVPATFQLCEEIVAAGGVIANVGVHGV-KADLHLEKLWDRNIAITTRLVDT 293

Query: 301 NTYPKGIEFLASGIVDTKHLVTDQYSLEQTQDAMERALQ-FKNECLKVMVYP 351
            + P  ++ + +G +D   L+T ++ L++  +A     Q    + LKV++ P
Sbjct: 294 ASTPMLLKTVQAGKLDPLKLITHRFKLDEALEAYRTFGQAAATQALKVIITP 345


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: 288
Number of extensions: 14
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: 345
Length adjustment: 29
Effective length of query: 324
Effective length of database: 316
Effective search space:   102384
Effective search space used:   102384
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 24 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