GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Dechlorosoma suillum PS

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate Dsui_1122 Dsui_1122 dihydroxy-acid dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__PS:Dsui_1122
          Length = 619

 Score =  207 bits (526), Expect = 1e-57
 Identities = 166/549 (30%), Positives = 252/549 (45%), Gaps = 55/549 (10%)

Query: 68  VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127
           +A+V+S+   +  H   +   + + + +   G + +    T A+ DG+  G  GM  SLP
Sbjct: 37  IAVVNSFTQFVPGHVHLKDLGQLVAREIEAAGGIAK-EFNTIAIDDGIAMGHDGMLYSLP 95

Query: 128 SREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSGISN 187
           SR++IA S    ++ +  DA + +  CDKI PG++M A+R  ++PTIFV GGPM +G   
Sbjct: 96  SRDLIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRV-NIPTIFVSGGPMEAGKVK 154

Query: 188 KE-------KADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
            E         D   +  +   +  E+ E E  +  + G+C+   TAN+   L E +GL 
Sbjct: 155 WEGKTIAVDLIDAMIKAGDSNCSDAEVEEFERSACPTCGSCSGMFTANSMNCLTEALGLS 214

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQ-----SGNFTPIGEIVDERSLVNSIVALH 295
           LPG   +      R  L  EA +++ RL ++       +  P   I ++++  N+     
Sbjct: 215 LPGNGTLVATHADRKGLFLEAGRRIVRLAQRWYEENDASVLP-RSIANQKAFENAFALDV 273

Query: 296 ATGGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYP-NGKADINHFQAAGGMA 354
           A GGSTN  LH+ A AQ AG+  T  D+  +S  VP L  V P      I     AGG+ 
Sbjct: 274 AMGGSTNTVLHLLATAQEAGVTFTMADIDAISRKVPCLCKVAPATQDYHIEDVHRAGGIM 333

Query: 355 FLIRELLEAGLLHEDVNTV----AGRGLSRY----------------------TQEPFLD 388
            ++ EL   GL+H D  TV     G  +  Y                      TQ  F  
Sbjct: 334 AILGELSRGGLIHRDTPTVHCHTLGEAIDTYDVQRAGSQRTLEFFRAAPGGIPTQTAFSQ 393

Query: 389 NGKLVWRDGPIESLDENILRPVARAFSPEGGLRVMEGNLGRGVMKVSAVALQHQI--VEA 446
           + +    D   +      +R VA A+S EGGL V+ GN+      V    +   I     
Sbjct: 394 DRRYTELD---QDRSNGCIRNVAHAYSKEGGLAVLHGNIALDGCIVKTAGVDESIWKFTG 450

Query: 447 PAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRSNGMPELHKMTPFLGVLQDRGF--KV 504
            A V++ Q     A   GE+    V V+R++GP+  G P + +M      L+ RG   + 
Sbjct: 451 KAKVYESQDSAVTAILGGEVVAGDVVVIRYEGPK--GGPGMQEMLYPTSYLKSRGLGKEC 508

Query: 505 ALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKV---DADE 561
           AL+TDGR SG +  +    H SPEA  GGA+  VR GD I +D     + L V   + ++
Sbjct: 509 ALLTDGRFSGGTSGLSIG-HASPEAAEGGAIGLVRTGDTIEIDIPGRRIHLAVSDAELEK 567

Query: 562 FAAREPAKG 570
             A E AKG
Sbjct: 568 RRAEENAKG 576


Lambda     K      H
   0.318    0.134    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: 940
Number of extensions: 51
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: 619
Length adjustment: 37
Effective length of query: 571
Effective length of database: 582
Effective search space:   332322
Effective search space used:   332322
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 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:

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