GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Halomonas xinjiangensis TRM 0175

Align D-xylulose reductase; Xylitol dehydrogenase; XDH; EC 1.1.1.9 (characterized)
to candidate WP_043527898.1 JH15_RS05915 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase

Query= SwissProt::Q07993
         (356 letters)



>NCBI__GCF_000759345.1:WP_043527898.1
          Length = 369

 Score = 99.8 bits (247), Expect = 1e-25
 Identities = 103/370 (27%), Positives = 157/370 (42%), Gaps = 50/370 (13%)

Query: 4   LTTQEAIVLERPGKITLTNVSI--PKISDPNEVIIQIKATGICGSDIHYYTHGRIANYVV 61
           + ++ A+ LE    + LT + +  PK     EV++QIKAT +C +D    +         
Sbjct: 1   MKSRAAVALEAGKPLELTEIEVDGPKAG---EVLVQIKATSVCHTDAFTLSGADPEGLF- 56

Query: 62  ESPMVLGHESSGIVALIGENVKTLKVGDRVALEPGIPDRFSPEMKEGRYNLDPNLKFAAT 121
             P VLGHE +GIV  +GE V +LK GD V     IP  ++ E  + ++ L       + 
Sbjct: 57  --PSVLGHEGAGIVQEVGEGVTSLKPGDHV-----IP-LYTAECGKCKFCLSGKTNLCSA 108

Query: 122 P----------------PFDGTLTKYYKTMKDFV-YKLPDDVSFEEGALIEPL------- 157
                              +G    +Y     F  Y +  +VS  + +   PL       
Sbjct: 109 VRATQGRGVMPDGTSRFSLNGQTLHHYMGCSTFSEYTVLPEVSLAKVSPEAPLDKICLLG 168

Query: 158 ---SVAIHA-NKLAKIKFGARCVVFGAGPIGLLAGKVASVFGAADVVFVDLLENKLETAR 213
              +  I A    AK++ G+   VFG G IGL   + A + GA+ ++ +D+  +K E AR
Sbjct: 169 CGVTTGIGAVMNTAKVEPGSTVAVFGLGAIGLAVIQGAQMVGASRIIAIDINADKFELAR 228

Query: 214 QFGATHIVNSGDLPHGVTVDSVIKKAIGKKGADVVFECSGAEPCVRAGIEVCKAG---GT 270
           QFGAT  VN  D  H   +  VI   +   G D  FEC G    +R  +E C  G     
Sbjct: 229 QFGATDFVNPKD--HADPIQQVIVD-MTDGGVDYSFECIGNVNVMRQALECCHKGWGESV 285

Query: 271 IVQVGMGQEEIQFPISIIPTKELTFQGCFRYCQG--DYSDSIELVSSRKLSLKPFITHRY 328
           I+ V    EEI      + T  +     F   +G  +    +E     ++ +  F+TH  
Sbjct: 286 IIGVAGAGEEISTRPFQLVTGRVWRGSAFGGVKGRTELPGYVERYMKGEIKIDEFVTHDM 345

Query: 329 SFKDAVEAFE 338
            F+   EAFE
Sbjct: 346 PFEQINEAFE 355


Lambda     K      H
   0.319    0.138    0.402 

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: 353
Number of extensions: 25
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 356
Length of database: 369
Length adjustment: 29
Effective length of query: 327
Effective length of database: 340
Effective search space:   111180
Effective search space used:   111180
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 (21.7 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