GapMind for Amino acid biosynthesis

 

Aligments 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)



>lcl|FitnessBrowser__Burk376:H281DRAFT_06137 H281DRAFT_06137
           dihydroxyacid dehydratase (EC 4.2.1.9)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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