GapMind for catabolism of small carbon sources

 

Aligments for a candidate for edd in Bacteroides thetaiotaomicron VPI-5482

Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate 351606 BT2078 dihydroxy-acid dehydratase (NCBI ptt file)

Query= curated2:P31961
         (608 letters)



>lcl|FitnessBrowser__Btheta:351606 BT2078 dihydroxy-acid dehydratase
           (NCBI ptt file)
          Length = 600

 Score =  214 bits (546), Expect = 6e-60
 Identities = 166/590 (28%), Positives = 271/590 (45%), Gaps = 42/590 (7%)

Query: 43  GNLAHGVAACGESDKQTLRLMNQANVAIVSAYNDMLSAHQPFERFPGLIKQALHEIGSVG 102
           G    G  A   ++      M +  +AIV+++   +  H        L+K  + ++G   
Sbjct: 13  GRRMAGARALWAANGMKKNQMGKPIIAIVNSFTQFVPGHVHLHEIGQLVKAEIEKLGCFA 72

Query: 103 QFAGGVPAMCDGVTQGEPGMELSLASRDVIAMSTAIALSHNMFDAALCLGVCDKIVPGLL 162
                + A+ DG+  G  GM  SL SRD+IA S    ++ +  DA +C+  CDKI PG+L
Sbjct: 73  AEFNTI-AIDDGIAMGHDGMLYSLPSRDIIADSVEYMVNAHKADAMVCISNCDKITPGML 131

Query: 163 IGSLRFGHLPTVFVPAGPMPTGISNKEKAAVRQLF---AEGKATREELLASEMASYHAPG 219
           + ++R  ++PTVFV  GPM  G  N +   +       A+   + +E+   E  +    G
Sbjct: 132 MAAMRL-NIPTVFVSGGPMEAGEWNGQHLDLIDAMIKSADDSVSDQEVANIEQNACPTCG 190

Query: 220 TCTFYGTANTNQLLVEVMGLHLPGASFVNPNTPLRDELTREAAR----QASRLTPENGNY 275
            C+   TAN+   L E +GL LPG   +      R +L  +AA+     A +   E    
Sbjct: 191 CCSGMFTANSMNCLNEAIGLALPGNGTIVATHENRTKLFEDAAKLIVENAMKYYEEGDES 250

Query: 276 VPMAEIVDEKAIVNSVVALLATGGSTNHTLHLLAIAQAAGIQLTWQDMSELSHVVPTLAR 335
           V    I   +A +N++   +A GGSTN  LHLLA+A  AG+     D+  LS   P L +
Sbjct: 251 VLPRSIATRQAFLNAMTLDIAMGGSTNTVLHLLAVAHEAGVDFKMDDIDMLSRKTPCLCK 310

Query: 336 IYPNGQA-DINHFQAAGGMSFLIRQLLDGGLLHEDVQTVAGPGLR--------------- 379
           + PN Q   I     AGG+  ++ +L  GGL+   V  V G  L                
Sbjct: 311 VAPNTQKYHIQDVNRAGGIIAILAELAKGGLIDTSVLRVDGMSLAEAIDQYSITSPNVTE 370

Query: 380 ----RYTREPFLEDGRLVWREGP-----ERSLDEAILRPLDKPFSAEGGLRLMEGNLGRG 430
               +Y+         ++  +G      ++      +R L+  +S +GGL +++GN+ + 
Sbjct: 371 KAMSKYSSAAGNRFNLVLGSQGAYYQELDKDRANGCIRDLEHAYSKDGGLAVLKGNIAQD 430

Query: 431 --VMKVSAVAPEHQVVEAPVRIFHDQASLAAAFKAGELERDLVAVVRFQGPRAN-GMPEL 487
             V+K + V         P ++F  Q +       G +    V V+  +GP+   GM E+
Sbjct: 431 GCVVKTAGVDESIWKFTGPAKVFDSQEAACEGILGGRVVSGDVVVITHEGPKGGPGMQEM 490

Query: 488 HKLTPFLGVLQDRGFKVALVTDGRMSGASGKVPAAIHVSPEAIAGGPLARLRDGDRVRVD 547
              T ++   +  G + AL+TDGR SG +  +    HVSPEA AGG + ++ DGD + +D
Sbjct: 491 LYPTSYIKS-RHLGKECALITDGRFSGGTSGLSIG-HVSPEAAAGGNIGKIVDGDIIEID 548

Query: 548 GVNGELRVLVDDAEWQARSLEPAPQDGNLGCGRELFAFMRNAMSSAEEGA 597
                + V + D E  AR + P  +D  +    + +A M   +SSA++GA
Sbjct: 549 IPARTINVRLTDEELAARPMTPVTRDRYVPKSLKAYASM---VSSADKGA 595


Lambda     K      H
   0.319    0.135    0.397 

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: 849
Number of extensions: 51
Number of successful extensions: 10
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: 608
Length of database: 600
Length adjustment: 37
Effective length of query: 571
Effective length of database: 563
Effective search space:   321473
Effective search space used:   321473
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: 53 (25.0 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 preprint 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