GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Brucella inopinata BO1

Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate WP_008506433.1 BIBO1_RS10395 dihydroxy-acid dehydratase

Query= curated2:P31961
         (608 letters)



>NCBI__GCF_000182725.1:WP_008506433.1
          Length = 611

 Score =  206 bits (524), Expect = 2e-57
 Identities = 162/545 (29%), Positives = 253/545 (46%), Gaps = 54/545 (9%)

Query: 68  VAIVSAYNDMLSAHQPFERFPGLIKQALHEIGSVGQFAGGVPAMCDGVTQGEPGMELSLA 127
           +A+V+++   +  H   +    L+ + +   G V +    + A+ DG+  G  GM  SL 
Sbjct: 37  IAVVNSFTQFVPGHVHLKDLGQLVAREIESAGGVAKEFNTI-AVDDGIAMGHDGMLYSLP 95

Query: 128 SRDVIAMSTAIALSHNMFDAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTG--- 184
           SR++IA S    ++ +  DA +C+  CDKI PG+L+ +LR  ++P VFV  GPM  G   
Sbjct: 96  SRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMAALRL-NIPVVFVSGGPMEAGKVV 154

Query: 185 ----ISNKEKAAVRQLFAEGKATREELLASEMASYHAPGTCTFYGTANTNQLLVEVMGLH 240
               +   +        A+   T E++ A E ++    G+C+   TAN+   L E +GL 
Sbjct: 155 WEDSVKKLDLVDAMVAAADDHYTDEQVKAIERSACPTCGSCSGMFTANSMNCLTEALGLS 214

Query: 241 LPGASFVNPNTPLRDELTREAARQ----ASRLTPENGNYVPMAEIVDEKAIVNSVVALLA 296
           LPG          R  L  EA       A R   ++   V    I    A  N++   +A
Sbjct: 215 LPGNGSTLATHADRKRLFVEAGHLIVDLARRYYEQDDESVLPRSIATFSAFENAMTLDIA 274

Query: 297 TGGSTNHTLHLLAIAQAAGIQLTWQDMSELSHVVPTLARIYPNGQA----DINHFQAAGG 352
            GGSTN  LHLLA AQ A I  T  D+  LS  VP L ++ P   +    D++H   AGG
Sbjct: 275 MGGSTNTVLHLLAAAQEAEIDFTMADIDRLSRRVPVLCKVAPAVSSVHMEDVHH---AGG 331

Query: 353 MSFLIRQLLDGGLLHEDVQTVAGPGLRR------------------YTREP--------F 386
           +  ++ QL + GLL   + TV    L +                  Y+  P        F
Sbjct: 332 IMGILGQLDNAGLLTTSIPTVHSETLAKALDHWDVTRTNSEMVHKFYSAAPGGVPTQVAF 391

Query: 387 LEDGRLVWREGPERSLDEAILRPLDKPFSAEGGLRLMEGNLGRG--VMKVSAVAPEHQVV 444
            ++ R    +  +   ++ ++R  +  FS +GGL ++ GNL     ++K + V       
Sbjct: 392 SQERRF---DKVDTDREKGVIRSKEHAFSQDGGLAVLYGNLAEDGCIVKTAGVDDSILKF 448

Query: 445 EAPVRIFHDQASLAAAFKAGELERDLVAVVRFQGPRAN-GMPELHKLTPFLGVLQDRGFK 503
             P RIF  Q S       G+++   + ++R++GPR   GM E+   T +L   +  G  
Sbjct: 449 SGPARIFESQDSAVLGILNGKIKPGDIVLIRYEGPRGGPGMQEMLYPTSYLKS-KGLGKA 507

Query: 504 VALVTDGRMSGASGKVPAAIHVSPEAIAGGPLARLRDGDRVRVDGVNGELRVLVDDAEWQ 563
            AL+TDGR SG S  +    HVSPEA  GG +  +R+GD + +D  N ++ + VDDA   
Sbjct: 508 CALITDGRFSGGSSGLSIG-HVSPEAAEGGTIGLVREGDIIDIDIPNRKIHLTVDDATLA 566

Query: 564 ARSLE 568
            R  E
Sbjct: 567 ERRAE 571


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: 867
Number of extensions: 46
Number of successful extensions: 9
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: 611
Length adjustment: 37
Effective length of query: 571
Effective length of database: 574
Effective search space:   327754
Effective search space used:   327754
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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