GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Paraburkholderia bryophila 376MFSha3.1

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate H281DRAFT_02329 H281DRAFT_02329 dihydroxyacid dehydratase

Query= curated2:A8AB39
         (552 letters)



>FitnessBrowser__Burk376:H281DRAFT_02329
          Length = 577

 Score =  395 bits (1014), Expect = e-114
 Identities = 224/546 (41%), Positives = 332/546 (60%), Gaps = 17/546 (3%)

Query: 15  HRALWRASGLIDEELR-RPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGT 73
           HR+  +  G+  +E   RP+IG+ N+W+E+ P + H  ++AE VK G+  AGG PLEF  
Sbjct: 27  HRSWMKNQGIPHDEFDGRPVIGICNTWSELTPCNAHFRELAEYVKKGVHEAGGLPLEFPV 86

Query: 74  IAVCDGIAMGHEGMR-YSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAAR 132
           ++      +G   +R  ++  R + +  VE  +  + +D V+++  CDK TP  L+ AA 
Sbjct: 87  MS------LGETNLRPTAMLFRNLASMDVEESIRGNPMDGVILLVGCDKTTPALLMGAAS 140

Query: 133 LEVPVILINGGPMMPGVYGKERIDFKDLMERMNVLIKEGRT--EELRKLEESALPGPGSC 190
             +P + ++GGPM+ G +  + I     + +M+  ++ G    EE  + E       G C
Sbjct: 141 CNLPALAVSGGPMLNGRFRGKHIGSGTGVWQMSEEVRAGSMTQEEFTEAESCMNRSRGHC 200

Query: 191 AGLFTANTMNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTR 250
             + TA+TM  + E++G+ LP  + +PAV+ARR   A L G RIV MV E LT DKILTR
Sbjct: 201 MTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGRRIVDMVREDLTMDKILTR 260

Query: 251 KALENAIAVDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFV 310
           +A ENAI  + A+GGSTN+V+HL ALA  +G++L LE + E+   VP + ++ PSG + +
Sbjct: 261 QAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDW-ELGSNVPCLVNLQPSGEYLM 319

Query: 311 VDLDRAGGIPAVLKELGEAGLIHKDALTVTGKTVWENVKDAAVLDREVIRPLDNPYSPFG 370
            D   AGG+PAVLK+LGE GL+H++ALTV GKT+W+NV++A   D +VI     P+ P  
Sbjct: 320 EDFYYAGGLPAVLKQLGEQGLLHREALTVNGKTIWDNVRNAPNHDEKVITTFAEPFKPKA 379

Query: 371 GLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAI--RGGEIEPGTVIVI 428
           G+A+LKG+LAPNGAV+K SA   EL K +G A VF+  E+    I     +I+   ++V+
Sbjct: 380 GIAVLKGNLAPNGAVIKPSAATAELLKHRGRAVVFENIEELHAKIDDESLDIDENCIMVL 439

Query: 429 RYEGPRGGPGMREM--LTATAAVMALGLGDKVALVTDGRFSGATRGPAIGHVSPEAAAGG 486
           +  GP+G PG  E+  +     V+  G+ D V  ++DGR SG   G  + HVSPEAAAGG
Sbjct: 440 KGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVR-ISDGRMSGTAYGAVVLHVSPEAAAGG 498

Query: 487 PIALVQDGDEIVIDIEKRRLDLLVDEKELEERRARWKPKVKPLRRGILRRYAKMALSADK 546
           P+A VQ GD I +D+E RRL L V + EL  RRA W+    P +RG  + Y +  L AD+
Sbjct: 499 PLAFVQTGDMIELDVEARRLHLDVSDDELARRRAAWQAPESP-KRGYYKLYVEHVLQADQ 557

Query: 547 GGALEY 552
           G  L++
Sbjct: 558 GADLDF 563


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: 824
Number of extensions: 37
Number of successful extensions: 7
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: 577
Length adjustment: 36
Effective length of query: 516
Effective length of database: 541
Effective search space:   279156
Effective search space used:   279156
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.

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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