GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dino:3607557
          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.

Links

Downloads

Related tools

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