GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuB in Klebsiella michiganensis M5al

Align D-mannonate oxidoreductase; EC 1.1.1.57; Fructuronate reductase (uncharacterized)
to candidate BWI76_RS19345 BWI76_RS19345 D-arabinitol 4-dehydrogenase

Query= curated2:P39160
         (486 letters)



>FitnessBrowser__Koxy:BWI76_RS19345
          Length = 455

 Score =  192 bits (489), Expect = 2e-53
 Identities = 138/443 (31%), Positives = 219/443 (49%), Gaps = 14/443 (3%)

Query: 26  VHLGCGAFHRAHQALYTHHLLESTDSDWGICEVNLMPGNDRVLIENLKKQ---QLLYTVA 82
           +H+G G+FHRAHQA Y H L+ S D  W I   N+    ++V ++ L  Q    +L TV+
Sbjct: 8   LHIGLGSFHRAHQAWYLHRLIASGDKRWHIAAGNIRNDAEQV-VQALAAQGGRYVLETVS 66

Query: 83  EKGAESTELKIIGSMKEALHPEIDGCEGILNAMARPQTAIVSLTVTEKGYCADAASGQLD 142
            +G    E + I S+++ L P   G + ++N  A PQT +++ TVTE GY  +    QL+
Sbjct: 67  PEGER--EYEEITSIQKLL-PWQAGLQPLINEGANPQTKVIAFTVTEGGYYLNTRH-QLE 122

Query: 143 LNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCDNVRENGHVAKVAVLGL 202
            +NP ++ DL      K+  G +   L  R        T+++CDNVR NG      ++  
Sbjct: 123 TSNPDLQADLAGEC--KTIYGTLARILEKRMADNAGPLTLLNCDNVRHNGERFHDGMVEF 180

Query: 203 AQARDPQLAA-WIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYDPCAIACEPFRQWV 261
            Q    Q    W+  N T P TMVDRI P    +    I  Q G+ D   +  E F QWV
Sbjct: 181 LQLTGKQAVIDWMAVNTTCPNTMVDRITPRPAADLPARIKAQTGIDDKAPVMGETFIQWV 240

Query: 262 IEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYLGGYETIADTVTNP 321
           +E+NF + RP  + VG + VA V+P+E  K+R+LN SHS +A+ G L G + I ++    
Sbjct: 241 VENNFRDERPKLEAVGVEMVASVIPYEEAKIRILNASHSCIAWAGTLIGQQYIHESTLTD 300

Query: 322 AYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTWQIAMDGSQKLPQR 381
                A   + ++  P L    G DL  Y  ++++RF+NP ++    ++A DG  K+P  
Sbjct: 301 FIYAIADRYVTEDVIPCLG-DNGIDLPTYRDVVLKRFTNPYIQDTNQRVAADGFSKIPAM 359

Query: 382 LLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPMLAEFQKINAQYQGAD 441
           +   ++   Q G      A+  A +  + +   +        D +L + Q ++  ++  D
Sbjct: 360 IAPTLQECYQRGVRPEATAMLPALFFVFMEQWHKGTLPYQYQDGIL-DAQAVHEMFEAQD 418

Query: 442 RVKALLGLSGIFADDLPQNADFV 464
            V AL   +      L  NADF+
Sbjct: 419 PV-ALYARNTALFGTLADNADFL 440


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: 563
Number of extensions: 22
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: 455
Length adjustment: 33
Effective length of query: 453
Effective length of database: 422
Effective search space:   191166
Effective search space used:   191166
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