GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Burk376:H281DRAFT_01519
          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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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