GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacD in Tistlia consotensis USBA 355

Align D-xylonate dehydratase subunit (EC 4.2.1.25; EC 4.2.1.82) (characterized)
to candidate WP_085125981.1 B9O00_RS27750 mandelate racemase/muconate lactonizing enzyme family protein

Query= metacyc::MONOMER-18070
         (393 letters)



>NCBI__GCF_900177295.1:WP_085125981.1
          Length = 400

 Score =  198 bits (504), Expect = 2e-55
 Identities = 125/386 (32%), Positives = 195/386 (50%), Gaps = 16/386 (4%)

Query: 3   KISEIEAYILGKEVTSAQWASLMVLVRVTTNDGRVGWGETVSA-LRAEAVANFVKKI-NT 60
           KI+++  +++G    S       V V++ T+ G  G GE          V   ++ +   
Sbjct: 2   KITDVRTFVVGNPPPSFG-GRYFVFVKLVTDGGVEGLGEVYCLPFHPRVVVAMIEDLAGR 60

Query: 61  VLKGNDVFNVEKNRLEWYKHDFNMTISLESTTAYSAVDIASWDIIGKELGAPLYKLLGGK 120
            L G D   +E      Y   +     L      S +++A WDI+GKE G P++ LLGG+
Sbjct: 61  YLVGQDPTRIESLWRRVYSAGYGQRPDLSVAGILSGLEMACWDILGKETGKPVHALLGGR 120

Query: 121 TRDKVLVYANGWYQNCVKPEDF-------AEKAKEIVKMGYKALKFDPFGPYF----NDI 169
             +++  Y    Y    +  DF       AE+A E V+ G+ A+KFDP GPY        
Sbjct: 121 VHERLRSYTY-LYPGEGETADFYHDAERSAERAAEYVRQGFTAIKFDPAGPYSAFDPRMP 179

Query: 170 SKKGLDIAEERVKAVREAVGDNVDILIEHHGRFNANSAIMIAKRLEKYNPLFMEEPIHPE 229
            ++ L  +E+  + +R AVG   D+L   HG+F    A+ +A+RLE Y+PL++EEP  PE
Sbjct: 180 DQESLARSEQFCRLIRAAVGGGADLLFGTHGQFTPAGALRLARRLEPYDPLWLEEPTPPE 239

Query: 230 DVEGLRKYRNNTSLRIALGERIINKQQALYFMKEGLVDFLQADLYRIGGVTETKKVVGIA 289
             E +      T++ +A GER+  K +    +  G    LQ +L R+GG+ E KK+ G+A
Sbjct: 240 MPEQMALVARGTTIPVAAGERLATKYEFARLLDAGAAAILQPNLGRVGGLLEAKKIAGLA 299

Query: 290 ETFDVQMAFHNAQGPILNAVTLQFDAFIPNFLIQESFYDWFPSWKRELIYNGTPIDNGYA 349
           E    Q+A H   GP++ A  +Q  A +PNFLI ES   W   +  EL+        GY 
Sbjct: 300 EARYAQVAPHLYCGPVVGAANIQLAATLPNFLILESIQTW-GGFHAELLKTPIRWQEGYV 358

Query: 350 IIPERPGLGVEVNEKMLDSLKVKGEE 375
           ++P+ PGLGVE++E +  +   +GEE
Sbjct: 359 LVPDAPGLGVELDEAVALAHPYEGEE 384


Lambda     K      H
   0.319    0.137    0.409 

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: 397
Number of extensions: 16
Number of successful extensions: 4
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: 393
Length of database: 400
Length adjustment: 31
Effective length of query: 362
Effective length of database: 369
Effective search space:   133578
Effective search space used:   133578
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 Apr 09 2024. 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