GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Dinoroseobacter shibae DFL-12

Align xylitol 2-dehydrogenase (EC 1.1.1.9) (characterized)
to candidate 3607669 Dshi_1078 Alcohol dehydrogenase zinc-binding domain protein (RefSeq)

Query= reanno::BFirm:BPHYT_RS16050
         (365 letters)



>FitnessBrowser__Dino:3607669
          Length = 345

 Score =  135 bits (341), Expect = 1e-36
 Identities = 106/341 (31%), Positives = 162/341 (47%), Gaps = 31/341 (9%)

Query: 22  KDYRVEQVSKPRAGAHELVIRIAACGICASDCKCHSGAKMFWGGPSPWVKAPVIPGHEFF 81
           +D  +E V +P      +V+++ ACG+C SD   H      W G  P VK   I GHE+ 
Sbjct: 11  EDLVLEDVPEPVCPEDGVVLKVLACGVCRSDW--HG-----WVGEHPRVKPGQIGGHEYC 63

Query: 82  GFVEEIGEGAADHFGVKMGDRVIAEQIVPCGKCRYCKSGQYWMCEVHNIFGFQREVADGG 141
           G V E G  AA     K GDRV+A  I+ CG C  C++G    C    + GF   V  G 
Sbjct: 64  GEVIEAGPRAA----FKPGDRVVAPFILACGSCPSCQAGAQNTCPNQRLPGF---VEPGA 116

Query: 142 MAEYMRIPPTAIVHKIPDGISLEDAAIIEPLACAIHTV-----NRGEVQLDDVVVIAGAG 196
            AEY+ +P    + ++PD +S   AA    L C + T       R  VQ  + V + G G
Sbjct: 117 FAEYVAVPFDHNLSRLPDSLSPTVAA---GLGCRVTTAWHALTGRAAVQGAEWVAVHGTG 173

Query: 197 PLGLMMTQIAHLKTPKKLVVIDLVEERLALAREYGADVTINPKQDDALAIIHSLTDGYGC 256
            +GL    +A+     +++ +D+V+E+L  A ++GA+VT+N ++ D  A I  +T G G 
Sbjct: 174 GIGLSSVILANA-LGARVIAVDVVDEKLTHAAQHGAEVTLNAREGDVAARIKQITGG-GA 231

Query: 257 DVYIETTGAPIGVNQGMDLIRKLGRFVEFSVFGADTT---LDWSVI--GDRKELDVRGAH 311
            V IE  G P  VN  ++ +R LGR V+  +    T    ++ S I  G+      RG  
Sbjct: 232 HVAIEALGIPETVNASLECLRPLGRHVQVGLPTGHTARMEINMSAIYQGNLAVYGTRG-- 289

Query: 312 LGPYCYPIAIDLLARGLVTSKGIVTHGFSLEEWDEAIKIAN 352
           +  + YP  + L+  G V    ++     L      ++  N
Sbjct: 290 MPSWRYPSLLSLIETGRVDMSPLIAREIGLSGTSAELRAFN 330


Lambda     K      H
   0.322    0.140    0.435 

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: 333
Number of extensions: 27
Number of successful extensions: 6
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: 365
Length of database: 345
Length adjustment: 29
Effective length of query: 336
Effective length of database: 316
Effective search space:   106176
Effective search space used:   106176
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: 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