GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Escherichia coli BW25113

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate 1937120 b3771 dihydroxy-acid dehydratase (NCBI)

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__Keio:1937120
          Length = 616

 Score =  221 bits (562), Expect = 9e-62
 Identities = 170/545 (31%), Positives = 265/545 (48%), Gaps = 42/545 (7%)

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

Query: 128 SREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSG--- 184
           SRE+IA S    ++ +  DA + +  CDKI PG++M +LR  ++P IFV GGPM +G   
Sbjct: 96  SRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMASLRL-NIPVIFVSGGPMEAGKTK 154

Query: 185 ----ISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
               I   +  D   + A+ K +  +  + E  +  + G+C+   TAN+   L E +GL 
Sbjct: 155 LSDQIIKLDLVDAMIQGADPKVSDSQSDQVERSACPTCGSCSGMFTANSMNCLTEALGLS 214

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTK----QSGNFTPIGEIVDERSLVNSIVALHA 296
            PG   +      R  L   A +++  LTK    Q+        I  + +  N++    A
Sbjct: 215 QPGNGSLLATHADRKQLFLNAGKRIVELTKRYYEQNDESALPRNIASKAAFENAMTLDIA 274

Query: 297 TGGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPN-GKADINHFQAAGGMAF 355
            GGSTN  LH+ A AQ A I  T  D+  LS  VP L  V P+  K  +     AGG+  
Sbjct: 275 MGGSTNTVLHLLAAAQEAEIDFTMSDIDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIG 334

Query: 356 LIRELLEAGLLHEDVNTVAGRGLSRYTQEPFL-----DNGKLVWRDGPI----------- 399
           ++ EL  AGLL+ DV  V G  L +  ++  +     D  K ++R GP            
Sbjct: 335 ILGELDRAGLLNRDVKNVLGLTLPQTLEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQD 394

Query: 400 ---ESLDEN----ILRPVARAFSPEGGLRVMEGNLGRGVMKVSAVALQHQIVE--APAVV 450
              ++LD++     +R +  A+S +GGL V+ GN       V    +   I++   PA V
Sbjct: 395 CRWDTLDDDRANGCIRSLEHAYSKDGGLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKV 454

Query: 451 FQDQQDLADAFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFKVALVTD 509
           ++ Q D  +A   G++    V V+R++GP+   GM E+   T FL  +   G   AL+TD
Sbjct: 455 YESQDDAVEAILGGKVVAGDVVVIRYEGPKGGPGMQEMLYPTSFLKSM-GLGKACALITD 513

Query: 510 GRMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFAAREPAK 569
           GR SG +  +    HVSPEA  GG++  + DGD+I +D     ++L+V   E AAR  A+
Sbjct: 514 GRFSGGTSGLSIG-HVSPEAASGGSIGLIEDGDLIAIDIPNRGIQLQVSDAELAARREAQ 572

Query: 570 GLLGN 574
              G+
Sbjct: 573 DARGD 577


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: 871
Number of extensions: 35
Number of successful extensions: 10
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: 616
Length adjustment: 37
Effective length of query: 571
Effective length of database: 579
Effective search space:   330609
Effective search space used:   330609
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