Aligments for a candidate for uxuB in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Aligments for a candidate for uxuB in Paraburkholderia bryophila 376MFSha3.1

Align D-mannonate oxidoreductase (EC 1.1.1.57) (characterized)
to candidate H281DRAFT_01519 H281DRAFT_01519 fructuronate reductase

Query= ecocyc::MANNONOXIDOREDUCT-MONOMER
         (486 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_01519 H281DRAFT_01519
           fructuronate reductase
          Length = 498

 Score =  395 bits (1016), Expect = e-114
 Identities = 213/464 (45%), Positives = 278/464 (59%), Gaps = 5/464 (1%)

Query: 25  IVHLGCGAFHRAHQALYTHHLLESTDSDWGICEVNLMPGNDRVLIENLKKQQLLYTVAEK 84
           IVHLG G FHRAHQALYT   + +   DWGIC V L    D      L +Q+ +Y+V E+
Sbjct: 37  IVHLGIGNFHRAHQALYTEEAMLAEGGDWGICGVTLQ--GDVAKRNALMEQEGVYSVVER 94

Query: 85  GAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVTEKGYCADAASGQLDLN 144
           G E  ++ ++ +++E L    D  + +   +A P   IVSLTVTEKGYC +A +G + L+
Sbjct: 95  GPEGAKVTVVRALREVLAMPHDH-DALFARLADPSVRIVSLTVTEKGYCRNAKTGDVALD 153

Query: 145 NPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCDNVRENGHVAKVAVLGLAQ 204
           NP + HDL +P AP+S  G +V ALR RR+   + FTV+SCDN+  NG   +  V   A+
Sbjct: 154 NPAVVHDLSHPHAPRSVPGILVAALRQRRDAAREPFTVLSCDNLAHNGAALRQVVCSFAR 213

Query: 205 ARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYDPCAIACEPFRQWVIED 264
             DP LA WI   V FP TMVDRI PA T      +A  LG  D   + CEPFRQWVIED
Sbjct: 214 EFDPALADWIAVEVAFPSTMVDRIAPATTDFEHATVAAALGYRDAAPVPCEPFRQWVIED 273

Query: 265 NFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYLGGYETIADTVTNPAYR 324
            F  GRP W  VGAQ V DV PFE+ KLRMLNG+HS LAYL  LGG+ TI + + +PA R
Sbjct: 274 RFPAGRPAWHAVGAQLVDDVTPFELAKLRMLNGTHSTLAYLSMLGGFTTIDEAIADPAMR 333

Query: 325 KAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTWQIAMDGSQKLPQRLLD 384
               A+M +E APTL+MP   D+  Y   L+ R++NP+L+HR  QIAMDGSQK+P RLL 
Sbjct: 334 NLIHAMMTEEIAPTLNMPASFDVANYRDALLARYANPALKHRCAQIAMDGSQKIPPRLLG 393

Query: 385 PVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPMLAEFQKINAQYQGADR-- 442
            +   +  G  +  LAL VAGWM + +G  + G+  D+ DP+    + + A   G  R  
Sbjct: 394 TIAARIDAGQPFTRLALAVAGWMTFLRGYADDGSRYDISDPLAENLKALAASANGDPRAL 453

Query: 443 VKALLGLSGIFADDLPQNADFVGAVTAAYQQLCERGARECVAAL 486
           +  LLG+  IF  +L     F  A+  A Q L + GAR  VAAL
Sbjct: 454 MDTLLGVREIFTAELAAQPAFRAALLHALQLLQDNGARAAVAAL 497


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: 678
Number of extensions: 30
Number of successful extensions: 4
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: 498
Length adjustment: 34
Effective length of query: 452
Effective length of database: 464
Effective search space:   209728
Effective search space used:   209728
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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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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