GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xad in Bacteroides clarus YIT 12056

Align D-xylonate dehydratase YagF; EC 4.2.1.82 (characterized)
to candidate WP_039951110.1 BUB52_RS01630 dihydroxy-acid dehydratase

Query= SwissProt::P77596
         (655 letters)



>NCBI__GCF_900129655.1:WP_039951110.1
          Length = 600

 Score =  198 bits (503), Expect = 7e-55
 Identities = 169/553 (30%), Positives = 262/553 (47%), Gaps = 61/553 (11%)

Query: 86  HTGHWEIGMQMQAAAKEITRNG--GIPFAAFVSDPCDGRSQGTHGMFDSLPYRNDAAIVF 143
           H    EIG  ++A   EI + G     F     D  DG + G  GM  SLP R+  A   
Sbjct: 51  HVHLHEIGQFVKA---EIEKQGCFAAEFNTIAID--DGIAMGHDGMLYSLPSRDIIADSV 105

Query: 144 RRLIRSLPTRRAVIGVATCDKGLPATMIALAAMHDLPTILVPGGATLPPTVGEDAGK-VQ 202
             ++ +     A++ ++ CDK  P  ++A   ++ +PT+ V GG   P   GE  G+ + 
Sbjct: 106 EYMVNAHKAD-AMVCISNCDKITPGMLMAAMRLN-IPTVFVSGG---PMEAGEWNGQHLD 160

Query: 203 TIGA--RFANHELSLQEAAELGCRACASPGGGCQFLGTAGTSQVVAEALGLALPHSALAP 260
            I A  + A+  +S  E A++   AC + G  C  + TA +   + EA+GLALP +    
Sbjct: 161 LIDAMIKSADESVSDNEVAKIEQHACPTCGC-CSGMFTANSMNCLNEAIGLALPGNGTIV 219

Query: 261 SGQAVWLEIARQSARAVSEL-------DSRGITTRDILSDKAIENAMVIHAAFGGSTNLL 313
           +      E+ + +A+ + E            +  R I + +A  NAM +  A GGSTN +
Sbjct: 220 ATHKNRKELFKDAAKLIVENAYKYYEEGDESVLPRSIATREAFLNAMTLDIAMGGSTNTV 279

Query: 314 LHIPAIAHAAGC--TIPDVEHWTRINRKVPRLVSVLPNGPDYHPTVRAFLAGGVPEVMLH 371
           LH+ A+AH AG   T+ D++    ++RK P L  V PN   YH       AGG+  +M  
Sbjct: 280 LHLLAVAHEAGADFTMDDID---MLSRKTPCLCKVAPNTQKYH-VQDVNRAGGIVAIMGE 335

Query: 372 LRDLGLLHLDAMTVTGQTVGENLEWW--------------QASERRARFRQCLREQDGVE 417
           L   GL+  +   V G T+ E ++ +               +S    +F   L  QD   
Sbjct: 336 LAKGGLVDTNVRRVDGMTLAEEIDRYCITDPNVCKEAIKKYSSAAAGKFNLVLGSQDAYY 395

Query: 418 PDDVILPPEKAK--------AKGLTSTVCFPTGNIAPEGSVIKATAIDPSVVGEDGVYHH 469
            +   L  ++A+        A      +    GNIA +G V+K   +D S+      +  
Sbjct: 396 KE---LDTDRAEGCIRDLQHAYSKDGGLAVLKGNIAQDGCVVKTAGVDESI------WKF 446

Query: 470 TGRVRVFVSEAQAIKAIKREEIVQGDIMVVIGGGPSG-TGMEETYQLTSALKHISWGKTV 528
           TG  +VF S+  A   I   ++V GD++V+   GP G  GM+E    TS +K    GK  
Sbjct: 447 TGPAKVFDSQEAACDGILGGKVVSGDVVVITHEGPKGGPGMQEMLYPTSYIKSRHLGKEC 506

Query: 529 SLITDARFSGVSTGACFGHVSPEALAGGPIGKLRDNDIIEIAVDRLTLTGSVNFIGTADN 588
           +LITD RFSG ++G   GH+SPEA AGG IGK++D DIIEI +   ++   +     A  
Sbjct: 507 ALITDGRFSGGTSGLSIGHISPEAAAGGNIGKIQDGDIIEIDIPNRSINVKLTDEELAAR 566

Query: 589 PLTPEEGARELAR 601
           P+TP    R++++
Sbjct: 567 PMTPVTRDRQVSK 579


Lambda     K      H
   0.319    0.136    0.411 

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: 941
Number of extensions: 40
Number of successful extensions: 7
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: 655
Length of database: 600
Length adjustment: 38
Effective length of query: 617
Effective length of database: 562
Effective search space:   346754
Effective search space used:   346754
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 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