GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoD in Pseudomonas fluorescens FW300-N1B4

Align galactonate dehydratase [EC: 4.2.1.6] (characterized)
to candidate Pf1N1B4_3383 Mandelate racemase (EC 5.1.2.2)

Query= reanno::BFirm:BPHYT_RS16405
         (382 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3383
          Length = 391

 Score =  134 bits (336), Expect = 6e-36
 Identities = 109/356 (30%), Positives = 174/356 (48%), Gaps = 35/356 (9%)

Query: 15  WCFLKIETDEGIVGWGEPVVEGRAHTVAAAVEELSDYL----IGKDPLLIEDHWQVMYRS 70
           W  +++ETD G+VG G   +  R      A E +  YL    IG+DP   E  WQ MYR 
Sbjct: 47  WLVVEVETDTGLVGIGNCALAPRV-----AKEIIDTYLAPIAIGEDPFDNEYIWQKMYRQ 101

Query: 71  GFYRGGP-ITMSAIAGVDQALWDIKGKHHGVPIHALLGGQVRDKIKVYS--WIGGDRPSD 127
               G   I M+AI+ +D A+WDI GK    P+  LLGG+ ++KI  Y+      D    
Sbjct: 102 SHAWGRKGIGMAAISAIDIAIWDIMGKAVNKPVFKLLGGRTKEKIWTYASKLYANDNLDL 161

Query: 128 VANNARAVVERGFKAVKMNGSEELQIIDTFDKVQGVINNVAAVREAVGPNIGIGVDFHGR 187
               A+  + +GF A+KM      +  D    ++  I  V A+RE  GP+I I ++ +  
Sbjct: 162 FLEEAQGYLNQGFTALKMRFGYGPK--DGPAGMRKNIEQVRALRELAGPDIDIMLECYMG 219

Query: 188 VHKPMAKVLAKELDPYKLLFIEEPVLSENAEALRDIVNQTNTPIALGERLYSRWDFKHIL 247
                A+ +  +L  ++  ++EEPV++++ E   ++      PI+ GE  ++ + FK +L
Sbjct: 220 WTLEYARRMLPKLAEFEPRWLEEPVIADDIEGYIELKKMGIMPISGGEHEFTSYGFKDLL 279

Query: 248 SGGYVDIIQPDASHAGGITECRKIASMAEAYDVALALHCPL---GPIALATCLQIDAVSY 304
               +D+IQ D +  GGIT  RKI ++AEA+ V +  H        + ++T     A  +
Sbjct: 280 ERRAIDVIQYDTNRVGGITAARKINALAEAWSVPVIPHAGQMHNYHLTMSTTASPMAEFF 339

Query: 305 NAFIQEQSLGIHYNQGNDLLDYIKNPEVFKYE----DGFVSIPQG-PGLGIEVNEE 355
             F  E         GN+L  Y     VFK E     G++ +    PGLG+E+++E
Sbjct: 340 PVFDVE--------VGNELFYY-----VFKGEPQPVKGYIQLDDNKPGLGLEISDE 382


Lambda     K      H
   0.319    0.139    0.428 

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: 444
Number of extensions: 27
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: 382
Length of database: 391
Length adjustment: 30
Effective length of query: 352
Effective length of database: 361
Effective search space:   127072
Effective search space used:   127072
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 (21.7 bits)
S2: 50 (23.9 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