GapMind for catabolism of small carbon sources

 

Aligments for a candidate for uxuA in Burkholderia phytofirmans PsJN

Align D-galactonate dehydratase family member Dd703_0947; EC 4.2.1.-; D-gluconate dehydratase; EC 4.2.1.39; D-mannonate dehydratase; EC 4.2.1.8 (uncharacterized)
to candidate BPHYT_RS16405 BPHYT_RS16405 galactonate dehydratase

Query= curated2:C6CBG9
         (417 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS16405 BPHYT_RS16405 galactonate
           dehydratase
          Length = 382

 Score =  195 bits (496), Expect = 2e-54
 Identities = 134/394 (34%), Positives = 208/394 (52%), Gaps = 48/394 (12%)

Query: 4   LKITNVKTILTAPGGIDLAVVKVETNEPGLYGLGCATFTQRIFAVKSAIDEYMAPFLIGK 63
           +KIT ++T +  P    L   K+ET+E G+ G G      R   V +A++E ++ +LIGK
Sbjct: 1   MKITKLETFIVPPRWCFL---KIETDE-GIVGWGEPVVEGRAHTVAAAVEE-LSDYLIGK 55

Query: 64  DPTRIEDIWQSAAVSGYWRNGPIMNNALSGVDMALWDIKGKLAGMPVYELLGGKCRDGIP 123
           DP  IED WQ    SG++R GPI  +A++GVD ALWDIKGK  G+P++ LLGG+ RD I 
Sbjct: 56  DPLLIEDHWQVMYRSGFYRGGPITMSAIAGVDQALWDIKGKHHGVPIHALLGGQVRDKIK 115

Query: 124 LYCHTDGGDEVEVEDNIRARMEEGYQYVRCQMGMYGGAGTDDLKLIATQLARAKNIQPKR 183
           +Y    G    +V +N RA +E G++ V+         G+++L++I T            
Sbjct: 116 VYSWIGGDRPSDVANNARAVVERGFKAVKMN-------GSEELQIIDT------------ 156

Query: 184 SPRSKTPGIYFDP-EAYAKSVPRLFEHLRNKLGFGIEFIHDVHERVTPVTAIQLAKTLEP 242
                     FD  +    +V  + E +   +G G++F    H RV    A  LAK L+P
Sbjct: 157 ----------FDKVQGVINNVAAVREAVGPNIGIGVDF----HGRVHKPMAKVLAKELDP 202

Query: 243 YQLFYLEDPVAPENIDWLRMLRQQSSTPISMGELFVNINEWKPLIDNKLIDYIRCHVSTI 302
           Y+L ++E+PV  EN + LR +  Q++TPI++GE   +  ++K ++    +D I+   S  
Sbjct: 203 YKLLFIEEPVLSENAEALRDIVNQTNTPIALGERLYSRWDFKHILSGGYVDIIQPDASHA 262

Query: 303 GGITPAKKLAVYSELNGVRTAWHGPGDISPVGVCANMHLDMSSPNFGIQE------YTPM 356
           GGIT  +K+A  +E   V  A H P  + P+ +   + +D  S N  IQE      Y   
Sbjct: 263 GGITECRKIASMAEAYDVALALHCP--LGPIALATCLQIDAVSYNAFIQEQSLGIHYNQG 320

Query: 357 NDALREV-FPGCPEIDQGYAYVNDKPGLGIDINE 389
           ND L  +  P   + + G+  +   PGLGI++NE
Sbjct: 321 NDLLDYIKNPEVFKYEDGFVSIPQGPGLGIEVNE 354


Lambda     K      H
   0.319    0.139    0.430 

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: 459
Number of extensions: 25
Number of successful extensions: 3
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: 417
Length of database: 382
Length adjustment: 31
Effective length of query: 386
Effective length of database: 351
Effective search space:   135486
Effective search space used:   135486
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 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