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

Query= curated2:P39160
         (486 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_04152 H281DRAFT_04152
           D-arabinitol 4-dehydrogenase
          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 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