GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuB in Pseudomonas fluorescens FW300-N2C3

Align D-mannonate oxidoreductase (EC 1.1.1.57) (characterized)
to candidate AO356_28535 AO356_28535 mannitol dehydrogenase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_28535
          Length = 485

 Score =  389 bits (998), Expect = e-112
 Identities = 223/458 (48%), Positives = 281/458 (61%), Gaps = 7/458 (1%)

Query: 25  IVHLGCGAFHRAHQALYTH-HLLESTDSDWGICEVNLMPGNDRVLIENLKKQQLLYTVAE 83
           IVHLG GAFHRAHQA+Y   HL    +SDWG+C  NL   ++R L+E L++Q   Y VAE
Sbjct: 18  IVHLGLGAFHRAHQAVYLQRHLNRHGESDWGVCSANLR--SNRTLVEQLREQDGRYHVAE 75

Query: 84  -KGAESTELKIIGSMKEALHPEIDG--CEGILNAMARPQTAIVSLTVTEKGYCADAASGQ 140
            +  E   L+ IG +++AL+    G   E +L  MA PQT IV+LTVTEKGYC   +SGQ
Sbjct: 76  YRDCEQVTLREIGVLRQALYVGEGGPDLEQLLMRMAAPQTRIVTLTVTEKGYCLSPSSGQ 135

Query: 141 LDLNNPLIKHDLENPTAPKSAIGYIVEALRLRREKGLKAFTVMSCDNVRENGHVAKVAVL 200
           L   +P I HDL +P AP+SA G ++EALR RR  G+ AFTV+ CDN+ +NG   + AV 
Sbjct: 136 LRSEDPAIAHDLAHPQAPRSAPGIVLEALRRRRAAGVPAFTVLCCDNMPDNGQRTRQAVS 195

Query: 201 GLAQARDPQLAAWIEENVTFPCTMVDRIVPAATPETLQEIADQLGVYDPCAIACEPFRQW 260
            LA  +D  LA W+E+ V FP  MVDRIVPA   E+ + + +QL  +DP A+ CE F QW
Sbjct: 196 ALAALQDEALAQWVEQQVAFPSCMVDRIVPAMDGESFRRL-EQLDCHDPAAVVCESFSQW 254

Query: 261 VIEDNFVNGRPDWDKVGAQFVADVVPFEMMKLRMLNGSHSFLAYLGYLGGYETIADTVTN 320
           VIED+F  GRPDW+  G Q V DV PFE MKLRMLNGSHS LAY+G L G++T+ + V++
Sbjct: 255 VIEDHFPLGRPDWEVEGVQMVDDVGPFETMKLRMLNGSHSLLAYVGLLVGHDTVFEAVSD 314

Query: 321 PAYRKAAFALMMQEQAPTLSMPEGTDLNAYATLLIERFSNPSLRHRTWQIAMDGSQKLPQ 380
                     M  E APTL MP G DL+ YA  L  RF+N SL+HR  QIAMDGSQKLPQ
Sbjct: 315 ANLLHLIGRYMADEAAPTLDMPAGIDLSVYAHDLKARFANDSLQHRLRQIAMDGSQKLPQ 374

Query: 381 RLLDPVRLHLQNGGSWRHLALGVAGWMRYTQGVDEQGNAIDVVDPMLAEFQKINAQYQGA 440
           R L   +  L  G      ALG+A W+ Y         A  V DP+ A F  +  +++GA
Sbjct: 375 RWLLGAQQLLDQGRGIDCTALGIAAWIHYCTQPLPGRPAHVVDDPLSATFADLAGRFEGA 434

Query: 441 DRVKALLGLSGIFADDLPQNADFVGAVTAAYQQLCERG 478
            RV A+L L  +F   L   A F  AV  AY  L   G
Sbjct: 435 SRVDAVLDLHEVFPPRLSARAVFRDAVHHAYSALTRDG 472


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: 681
Number of extensions: 40
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 486
Length of database: 485
Length adjustment: 34
Effective length of query: 452
Effective length of database: 451
Effective search space:   203852
Effective search space used:   203852
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.

Links

Downloads

Related tools

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