Aligments for a candidate for uxuB in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Aligments for a candidate for uxuB in Dinoroseobacter shibae DFL-12

Align D-mannonate oxidoreductase; EC 1.1.1.57; Fructuronate reductase (uncharacterized)
to candidate 3607557 Dshi_0969 Mannitol dehydrogenase domain (RefSeq)

Query= curated2:P39160
         (486 letters)



>lcl|FitnessBrowser__Dino:3607557 Dshi_0969 Mannitol dehydrogenase
           domain (RefSeq)
          Length = 499

 Score =  297 bits (760), Expect = 6e-85
 Identities = 187/480 (38%), Positives = 261/480 (54%), Gaps = 12/480 (2%)

Query: 9   LPVARPSWDHSRLESRIVHLGCGAFHRAHQALYTHHLLESTDS-DWGICEVNLMPGNDRV 67
           L + RP +D SRL   IVH+G G FHRAHQA Y H L+++  + DW I    + P  D  
Sbjct: 15  LAIERPRYDRSRLTPGIVHIGVGNFHRAHQAWYLHRLMQAGQALDWAIIGAGVRP-YDAA 73

Query: 68  LIENLKKQQLLYTVAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTV 127
           + + L  Q  L T+ E   ++   +++GSM + L P +DG   ++  MA P   IV++TV
Sbjct: 74  MRDKLLAQDCLTTLIELAPDNVSAEVVGSMIDYL-PIVDGNGPLIAQMADPAIRIVAMTV 132

Query: 128 TEKGYCADAASGQLDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCDN 187
           TE GY  D  +   D ++P + HD   P  P++A G IV ALR RR  G   FT +SCDN
Sbjct: 133 TESGYYIDPVTKGFDASHPDLVHDAAQPDRPRTAFGAIVAALRARRAAGHGPFTCLSCDN 192

Query: 188 VRENGHVAKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVY 247
           ++ NG + +  V+ LA+  DP LA WI+ + +FP +MVD I PA  P+ L  +A Q G+ 
Sbjct: 193 LQGNGDILRQTVVSLARLTDPALADWIDTHASFPNSMVDCIAPATGPKELA-LAAQFGIR 251

Query: 248 DPCAIACEPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGY 307
           D   +  E FRQWVIED F  GRP+WD VGA F  DV  +E MK+R+LN  H  LA  G 
Sbjct: 252 DVAVVTHEAFRQWVIEDEFCAGRPNWDAVGATFSDDVHAYETMKIRILNAGHQVLANAGE 311

Query: 308 LGGYETIADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRT 367
             G ETI+  + +P        +  +E APT++   G    +Y  L+  RF+NP +   T
Sbjct: 312 NLGIETISGCMAHPGIAAFFGKVQREEIAPTVAPVPGKTPASYVNLIETRFANPRIVDTT 371

Query: 368 WQIAMDGSQKLPQRLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPML 427
            ++A DGS + P  +L  VR  L  G S   LAL  A W R   GV E G  I   DP+ 
Sbjct: 372 RRVAFDGSARHPGFVLPIVRDQLAAGRSVEGLALVEALWARMCAGVREDGTEIAPNDPL- 430

Query: 428 AEFQKINAQYQGADRVKAL-LGLSGIFADDLPQNADFVGAVTAAYQQLCERGARECVAAL 486
             + ++    + A    AL LG +G++  DL Q+  F  A  A    + ++G   C AAL
Sbjct: 431 --WDRLAPVARAARTDPALWLGQTGLYG-DLKQSEPFADAFCAWLVLIWDKG---CEAAL 484


Lambda     K      H
   0.320    0.135    0.408 

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: 655
Number of extensions: 32
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: 486
Length of database: 499
Length adjustment: 34
Effective length of query: 452
Effective length of database: 465
Effective search space:   210180
Effective search space used:   210180
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: 52 (24.6 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources