GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__PS:Dsui_1122 Dsui_1122 dihydroxy-acid
           dehydratase
          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 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