GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Bacteroides clarus YIT 12056

Align Phosphogluconate dehydratase; EC 4.2.1.12 (uncharacterized)
to candidate WP_039951110.1 BUB52_RS01630 dihydroxy-acid dehydratase

Query= curated2:P56111
         (608 letters)



>NCBI__GCF_900129655.1:WP_039951110.1
          Length = 600

 Score =  207 bits (528), Expect = 8e-58
 Identities = 162/529 (30%), Positives = 261/529 (49%), Gaps = 42/529 (7%)

Query: 69  AIITAYNDMLSAHQPFKNYPDLIKKELQEHNAYASVASGVPAMCDGITQGYDGMELSLFS 128
           AI+ ++   +  H         +K E+++   +A+  + + A+ DGI  G+DGM  SL S
Sbjct: 39  AIVNSFTQFVPGHVHLHEIGQFVKAEIEKQGCFAAEFNTI-AIDDGIAMGHDGMLYSLPS 97

Query: 129 RDVIALSTAVGLSHNVFDGAFFLGVCDKIVPGLLIGALSFGNLASVFVPSGPMVSGIENY 188
           RD+IA S    ++ +  D    +  CDKI PG+L+ A+   N+ +VFV  GPM +G  N 
Sbjct: 98  RDIIADSVEYMVNAHKADAMVCISNCDKITPGMLMAAMRL-NIPTVFVSGGPMEAGEWNG 156

Query: 189 KKAK---ARQDFAMGKINREELLKVEMQSYHDVGTCTFYGTANSNQMMMEFMGLHVANSS 245
           +      A    A   ++  E+ K+E  +    G C+   TANS   + E +GL +  + 
Sbjct: 157 QHLDLIDAMIKSADESVSDNEVAKIEQHACPTCGCCSGMFTANSMNCLNEAIGLALPGNG 216

Query: 246 FINPNNPLRKVLVEESAKRLASG----------KVLPLAKLIDEKSILNALIGLMATGGS 295
            I   +  RK L +++AK +              VLP + +   ++ LNA+   +A GGS
Sbjct: 217 TIVATHKNRKELFKDAAKLIVENAYKYYEEGDESVLPRS-IATREAFLNAMTLDIAMGGS 275

Query: 296 TNHTLHLIAIARSCGVILNWDDFDAVSNLIPLLAKVYPNGSA-DVNAFEACGGLVFVIKE 354
           TN  LHL+A+A   G     DD D +S   P L KV PN     V      GG+V ++ E
Sbjct: 276 TNTVLHLLAVAHEAGADFTMDDIDMLSRKTPCLCKVAPNTQKYHVQDVNRAGGIVAIMGE 335

Query: 355 LLKEGLLFE--------------DTHTIMDTET-QKGMQNYTKTPFLENNQLV-YKDAIN 398
           L K GL+                D + I D    ++ ++ Y+     + N ++  +DA  
Sbjct: 336 LAKGGLVDTNVRRVDGMTLAEEIDRYCITDPNVCKEAIKKYSSAAAGKFNLVLGSQDAYY 395

Query: 399 HSLNTD----ILRPVSDPFAANGGLKILKGNLGR--AVIKISAIKDEHRKVKARAIVFKT 452
             L+TD     +R +   ++ +GGL +LKGN+ +   V+K + + +   K    A VF +
Sbjct: 396 KELDTDRAEGCIRDLQHAYSKDGGLAVLKGNIAQDGCVVKTAGVDESIWKFTGPAKVFDS 455

Query: 453 QSEFLERFKNKELERDFVAVLPFQGPKSN-GMPELHKLTTNLGALQDMGYKVALVTDGRM 511
           Q    +     ++    V V+  +GPK   GM E+   T+ + + + +G + AL+TDGR 
Sbjct: 456 QEAACDGILGGKVVSGDVVVITHEGPKGGPGMQEMLYPTSYIKS-RHLGKECALITDGRF 514

Query: 512 SGASGKVPSAIHLSPEGALNGAIIKIKDGDLIELDAPNNALNVLEKDFE 560
           SG +  + S  H+SPE A  G I KI+DGD+IE+D PN ++NV   D E
Sbjct: 515 SGGTSGL-SIGHISPEAAAGGNIGKIQDGDIIEIDIPNRSINVKLTDEE 562


Lambda     K      H
   0.318    0.135    0.386 

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: 779
Number of extensions: 41
Number of successful extensions: 6
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: 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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 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