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_06137 H281DRAFT_06137 dihydroxyacid dehydratase (EC 4.2.1.9)

Query= curated2:B9MPM8
         (552 letters)



>FitnessBrowser__Burk376:H281DRAFT_06137
          Length = 583

 Score =  362 bits (928), Expect = e-104
 Identities = 212/547 (38%), Positives = 314/547 (57%), Gaps = 14/547 (2%)

Query: 8   KGFEKAPQRSLFKAMGYTDEEIRRPLIAVVNSWNEVVPGHIHLDRIAEAVKAGIRLAGAT 67
           +GF    +++  K  GYTD+ + RP+I +VN+ +     H ++ ++ EAVK G+ LAG  
Sbjct: 27  QGFSLFLRKAFIKGAGYTDQALDRPVIGIVNTGSGFNACHGNMPQLVEAVKRGVMLAGGL 86

Query: 68  PMEFNVIGVCDGIAMGHIGMKYSLITRELIADSIEAMVMAHQFDGMVLIPNCDKIVPGML 127
           P++F  I V +  +        S+  R L++   E M+ A   D +VLI  CDK VP  L
Sbjct: 87  PVDFPTISVHESFSS-----PTSMYLRNLMSMDTEEMIRAQPMDAVVLIGGCDKTVPAQL 141

Query: 128 IAAARVNIPAILISGGPMLAGKI-GDKVCDLNSVFEGVGAYSAGKISEEDLYALEENACP 186
           + AA   IPAI +  G ML G    ++V          G + A +I +E++  +      
Sbjct: 142 MGAASAEIPAIQLVTGSMLTGSHRSERVGACTDCRRYWGKFRASEIDQEEINDVNNQLVA 201

Query: 187 GCGSCSGMFTANTMNCLSEVLGLALPGNGTIPAVMAARIRLAKMAGMKIVELVEKDIKPS 246
             G+CS M TA+TM C++E LG+ +PG  T PAV A RIR+A+  G   V+L  + +   
Sbjct: 202 SVGTCSVMGTASTMACIAEALGMTVPGGATPPAVTADRIRVAEQTGTTAVKLASERLTID 261

Query: 247 DILTVEAFENALAVDMALGGSTNTILHLPAIANEVGIKLNLDIINAISDRTPNLCKLSPA 306
            ILT +AFENA+ V +A+GGSTN I+HL A+A  +G K+ LD ++ +   TP L  L P 
Sbjct: 262 KILTPKAFENAMRVLLAIGGSTNAIVHLSAVAGRLGHKIGLDSLDRMGKETPVLLDLKPT 321

Query: 307 GQHHIEDLYFAGGVQAVMNELSKKGLLHLNLMTVTGKTVGENIKDANVK-NYNVIRPIDN 365
           GQH++ED + AGGV  ++ EL  K LLHL+ MTV+G T+GE I+ +    + +V+R    
Sbjct: 322 GQHYMEDFHKAGGVATLLREL--KPLLHLDAMTVSGHTLGEQIEASGPGFSQDVVRSFSQ 379

Query: 366 PYSETGGLVIVRGNLAPDGAVVKKSAVPPKLMKHRGPARVFESGEEVFEAILKGK--IQK 423
           P    GGL +VRGNLAP GA++K+SA  PKLM+H G A VFE+ E++   +      ++ 
Sbjct: 380 PIYPQGGLAVVRGNLAPGGAIIKQSAADPKLMEHEGRAVVFENLEDLINRVDDESLDVKA 439

Query: 424 GDVIVIRYEGPKGGPGMRE--MLSPTSALAGVGLIEDVALITDGRFSGATRGACFGHVSP 481
            DV+V++  GP G PGM E   +     LA  G ++D+  I+DGR SG   G    HV+P
Sbjct: 440 DDVLVLKNIGPVGAPGMPEAGYIPIPRKLARAG-VKDMVRISDGRMSGTAFGTIVLHVTP 498

Query: 482 EAAERGPIAAVQDGDMISIDIENKTLTLEVPEEEIKRRLEILPPFEPKVKKGYLYRYSKL 541
           EAA  GP A VQ+GD I + + N+ ++L V +E++K+R    P   P   +GY   + + 
Sbjct: 499 EAAAGGPFAYVQNGDRIRLSVSNREVSLLVSDEKLKQRAADKPIKRPTADRGYRKLFLQT 558

Query: 542 VRSASTG 548
           V  A  G
Sbjct: 559 VTQADEG 565


Lambda     K      H
   0.318    0.137    0.394 

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: 806
Number of extensions: 50
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: 583
Length adjustment: 36
Effective length of query: 516
Effective length of database: 547
Effective search space:   282252
Effective search space used:   282252
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 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