GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Escherichia coli BW25113

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate 15969 b1851 phosphogluconate dehydratase (NCBI)

Query= curated2:A8AB39
         (552 letters)



>FitnessBrowser__Keio:15969
          Length = 603

 Score =  249 bits (637), Expect = 2e-70
 Identities = 171/523 (32%), Positives = 267/523 (51%), Gaps = 49/523 (9%)

Query: 27  EELRRPLIGVANSWNEIVPGHVHLDKVAEAVKAGI-------RMAGGTPLEFGTIAVCDG 79
           + + R  I +  S+N+++  H   +   E ++  +       ++AGG P      A+CDG
Sbjct: 61  KSMLRNNIAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVP------AMCDG 114

Query: 80  IAMGHEGMRYSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-EVPVI 138
           +  G +GM  SL SREVIA +  + +  +  D  + +  CDKI PG  +AA     +P +
Sbjct: 115 VTQGQDGMELSLLSREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLPAV 174

Query: 139 LINGGPMMPGVYGKERIDFKDLMERMNVLIKEGRTEELRKLEESALP--GPGSCAGLFTA 196
            +  GPM  G+  KE++       R+  L  EG+ + +  LE  A     PG+C    TA
Sbjct: 175 FVPSGPMASGLPNKEKV-------RIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTA 227

Query: 197 NTMNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEG---LTPDKILTRKAL 253
           NT  M+ E MG+ LPG+S V      R         ++ +M   G   +   K++  K +
Sbjct: 228 NTNQMVVEFMGMQLPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWMPIGKMIDEKVV 287

Query: 254 ENAIAVDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDL 313
            N I   +A GGSTN  +HL A+A   GI +  + F ++S  VP +A + P+G   +   
Sbjct: 288 VNGIVALLATGGSTNHTMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPNGPADINHF 347

Query: 314 DRAGGIPAVLKELGEAGLIHKDALTV---------------TGKTVWENVKDAAVLDREV 358
             AGG+P +++EL +AGL+H+D  TV                G+  W    + + LD  V
Sbjct: 348 QAAGGVPVLVRELLKAGLLHEDVNTVAGFGLSRYTLEPWLNNGELDWREGAEKS-LDSNV 406

Query: 359 IRPLDNPYSPFGGLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGG 418
           I   + P+S  GG  +L G+L    AV+K SAV  E    +  A VF+ + D + A   G
Sbjct: 407 IASFEQPFSHHGGTKVLSGNL--GRAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAG 464

Query: 419 EIEPGTVIVIRYEGPR--GGPGMREMLTATAAVMALGLGDKVALVTDGRFSGAT-RGPAI 475
            ++   V+V+R++GP+  G P + +++     +  L    K+ALVTDGR SGA+ + P+ 
Sbjct: 465 LLDRDCVVVVRHQGPKANGMPELHKLMPPLGVL--LDRCFKIALVTDGRLSGASGKVPSA 522

Query: 476 GHVSPEAAAGGPIALVQDGDEIVIDIEKRRLDLLVDEKELEER 518
            HV+PEA  GG +A V+DGD I ++ +   L LLVDE EL  R
Sbjct: 523 IHVTPEAYDGGLLAKVRDGDIIRVNGQTGELTLLVDEAELAAR 565


Lambda     K      H
   0.319    0.138    0.401 

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: 808
Number of extensions: 52
Number of successful extensions: 8
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: 552
Length of database: 603
Length adjustment: 36
Effective length of query: 516
Effective length of database: 567
Effective search space:   292572
Effective search space used:   292572
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 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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