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; Fructuronate reductase (uncharacterized)
to candidate H281DRAFT_04152 H281DRAFT_04152 D-arabinitol 4-dehydrogenase

Query= curated2:P39160
         (486 letters)



>FitnessBrowser__Burk376:H281DRAFT_04152
          Length = 470

 Score =  213 bits (541), Expect = 1e-59
 Identities = 138/365 (37%), Positives = 196/365 (53%), Gaps = 21/365 (5%)

Query: 25  IVHLGCGAFHRAHQALYTHHLLEST---DSDWGICEVNLMPGNDRVLIENLKKQQLLYT- 80
           I+H+G G+FHRAHQA Y H L E+    +  W +   N+    + VL E L  Q  +YT 
Sbjct: 14  ILHIGAGSFHRAHQAWYLHRLNEANLPGEPHWSLTVGNIRSDMNAVL-EALAAQDGVYTL 72

Query: 81  --VAEKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVTEKGYCADAAS 138
             V  +G  + E   I S++  + P  +  + ++ A A P   I+S TVTE GY  D   
Sbjct: 73  ETVTPQGERAYET--IRSIERVV-PWTESLDALIEAGADPACKIISFTVTEGGYYLDEHD 129

Query: 139 GQLDLNNPLIKHDLENP-TAPKSAIGYIVEALRLRREKGLKAFTVMSCDNVRENG---HV 194
            QLD  NP +  DL+   T    A+  I+EA   R + G    T+ +CDN+R NG   H 
Sbjct: 130 -QLDTANPDLSTDLKGGHTTIYGALAAILEA---RMKNGAGPVTLQTCDNLRRNGERFHA 185

Query: 195 AKVAVLGLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYDPCAIAC 254
              A L L  A +  LA W ++N   P +MVDRI P  TP+  + +    GV D C +  
Sbjct: 186 GMSAFLELRGAGE--LAQWFDDNTACPSSMVDRITPRPTPDVRERVKAATGVDDACPVMG 243

Query: 255 EPFRQWVIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYLGGYETI 314
           E F QWVIE+ F+ GRP W+KVGA+ V  V+P+E  K+R+LN +HS +A+ G L G   I
Sbjct: 244 EAFIQWVIEERFIAGRPAWEKVGAELVDSVLPYEEAKIRILNATHSCIAWAGTLVGLNYI 303

Query: 315 ADTVTNPAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTWQIAMDG 374
            +   +   RK AF  + ++  P LS P   DL  Y  +++ERF NP ++    ++A DG
Sbjct: 304 HEGTQDADIRKFAFDYVTEDVIPCLS-PSPLDLERYRDVVLERFGNPYIQDTNQRVAADG 362

Query: 375 SQKLP 379
             KLP
Sbjct: 363 FSKLP 367


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: 589
Number of extensions: 32
Number of successful extensions: 5
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: 470
Length adjustment: 34
Effective length of query: 452
Effective length of database: 436
Effective search space:   197072
Effective search space used:   197072
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: 51 (24.3 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