GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Sinorhizobium meliloti 1021

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate SM_b20890 SM_b20890 dihydroxy-acid dehydratase

Query= curated2:A8AB39
         (552 letters)



>FitnessBrowser__Smeli:SM_b20890
          Length = 579

 Score =  389 bits (998), Expect = e-112
 Identities = 219/546 (40%), Positives = 329/546 (60%), Gaps = 15/546 (2%)

Query: 15  HRALWRASGL-IDEELRRPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGT 73
           HR+  +  GL  D    RP+IG+ N+W+E+ P + HL  +AE VK G+  AGG P+EF  
Sbjct: 27  HRSWMKNQGLPADTFDGRPIIGICNTWSELTPCNAHLRDLAERVKRGVYEAGGFPVEFPV 86

Query: 74  IAVCDGIAMGHEGMR-YSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAAR 132
            +       G   +R  ++  R + A  VE  +  + +D VV++  CDK TP  L+ AA 
Sbjct: 87  FST------GESTLRPTAMMFRNLAAMDVEESIRGNPVDGVVLLGGCDKTTPSLLMGAAS 140

Query: 133 LEVPVILINGGPMMPGVYGKERIDFKDLMERMNVLIKEGRT--EELRKLEESALPGPGSC 190
           +++P I+++GGPM+ G +  + +     + + + ++K G    EE    E+      GSC
Sbjct: 141 VDIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEMVKSGEMSLEEFMDAEQGMARSAGSC 200

Query: 191 AGLFTANTMNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTR 250
             + TA+TM  ++EA+G+ L G + +PAV+ARR   ++LTG RIV+MV+E L P  ILT+
Sbjct: 201 MTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLTGRRIVEMVKEDLKPSDILTK 260

Query: 251 KALENAIAVDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFV 310
           +A ENAI V+ A+GGSTN+VLHL ALA  +G+DL L+ +D + R VP I ++ PSG++ +
Sbjct: 261 EAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWDRLGRDVPTIVNLQPSGKYLM 320

Query: 311 VDLDRAGGIPAVLKELGEAGLIHKDALTVTGKTVWENVKDAAVLDREVIRPLDNPYSPFG 370
            +   AGG+P V+K + E GL+H DA+TV+G T+W +VK     + +VI P +   +  G
Sbjct: 321 EEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTIWNDVKGVVNYNEDVILPREKALTKSG 380

Query: 371 GLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGG--EIEPGTVIVI 428
           G+A+L+G+LAP GAV+K SA    L + KG A VF+  ED    I     +I+   ++V+
Sbjct: 381 GIAVLRGNLAPRGAVLKPSAASPHLMQHKGRAVVFESIEDYHARINREDLDIDETCIMVL 440

Query: 429 RYEGPRGGPGMREM--LTATAAVMALGLGDKVALVTDGRFSGATRGPAIGHVSPEAAAGG 486
           +Y GP+G PGM E+  +     V+  G+ D +  ++D R SG   G  I H +PEAA GG
Sbjct: 441 KYCGPKGYPGMAEVGNMGLPPKVLKKGITDMIR-ISDARMSGTAYGTVILHTAPEAAEGG 499

Query: 487 PIALVQDGDEIVIDIEKRRLDLLVDEKELEERRARWKPKVKPLRRGILRRYAKMALSADK 546
           P+ALV++GD I +DI  R L L V ++EL  RRA W   VKPL  G    Y K  + AD 
Sbjct: 500 PLALVENGDLIEVDIPNRTLHLHVSDEELARRRAAWVSPVKPLTGGYGGLYIKTVMQADA 559

Query: 547 GGALEY 552
           G  L++
Sbjct: 560 GADLDF 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: 832
Number of extensions: 42
Number of successful extensions: 5
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: 579
Length adjustment: 36
Effective length of query: 516
Effective length of database: 543
Effective search space:   280188
Effective search space used:   280188
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