GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Pseudomonas fluorescens FW300-N2C3

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate AO356_28760 AO356_28760 dihydroxy-acid dehydratase

Query= curated2:A8AB39
         (552 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28760
          Length = 594

 Score =  303 bits (776), Expect = 1e-86
 Identities = 191/548 (34%), Positives = 301/548 (54%), Gaps = 26/548 (4%)

Query: 23  GLIDEELR--RPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTIAVCDGI 80
           G+  EEL+  RP+IG+A + +++ P + H  ++A+ VKAGIR AGG P+EF    + +  
Sbjct: 35  GMTREELQSGRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQS 94

Query: 81  AMGHEGMRYSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARLEVPVILI 140
                 +  +L         VEI+   + LD VV+ T CDK TP  L+AAA  ++P I++
Sbjct: 95  RRPTAALDRNL----AYLGLVEIL-HGYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVL 149

Query: 141 NGGPMMPGVYGKERIDFKDLMERMNVLIKEGRT--EELRKLEESALPGPGSCAGLFTANT 198
           +GGPM+ G +  E I    ++     L+  G    E   ++  +A P  G C  + TA +
Sbjct: 150 SGGPMLDGHHKGELIGSGTVLWHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMGTALS 209

Query: 199 MNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTRKALENAIA 258
           MN L+EA+G+ LPG +++PA    R   A  TG RI ++V + + P +I+TR+A ENAIA
Sbjct: 210 MNALAEALGMSLPGCASIPAPYRERGQMAYATGKRICELVLQDIRPSQIMTRQAFENAIA 269

Query: 259 VDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGG 318
           V  ALG S+N   HL A+A  +G++L L+ +  I   VP + +  P+G++      RAGG
Sbjct: 270 VASALGASSNCPPHLIAIARHMGVELSLDDWQRIGEDVPLLVNCMPAGKYLGEGFHRAGG 329

Query: 319 IPAVLKELGEAGLIHKDALTVTGKTVWENVKDAAVLDREVIRPLDNPYSPFGGLAILKGS 378
           +P+V+ EL +AG +H+D  TV+G+T+ E V  +   + +VI P D P     G  +L G+
Sbjct: 330 VPSVMHELQKAGRLHEDCATVSGRTIGEIVSSSLTSNADVIHPFDTPLKHRAGFIVLSGN 389

Query: 379 LAPNGAVVKASAVKRELWK-----------FKGVARVFDREEDAVKAIRGG--EIEPGTV 425
              + A++K S V     K           F+  A VF+  ED    I     +I+   +
Sbjct: 390 FF-DSAIMKMSVVGEAFRKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPALDIDERCI 448

Query: 426 IVIRYEGPRGGPGMREM--LTATAAVMALGLGDKVALVTDGRFSGATRGPAIGHVSPEAA 483
           +VIR  G  G PG  E+  +   AA++  G+ D +  + DGR SG +  P+I ++SPEAA
Sbjct: 449 LVIRGVGTVGYPGSAEVVNMAPPAALIKQGI-DSLPCLGDGRQSGTSASPSILNMSPEAA 507

Query: 484 AGGPIALVQDGDEIVIDIEKRRLDLLVDEKELEERRARWKPKVKPLRRGILRRYAKMALS 543
            GG +AL+Q  D + +D+  R ++LL+D++E+  RR  W P + P +      Y ++   
Sbjct: 508 VGGGLALLQTNDRLKVDLNTRTVNLLIDDEEMARRRLEWTPNIPPSQTPWQELYRQLVGQ 567

Query: 544 ADKGGALE 551
              GG LE
Sbjct: 568 LSTGGCLE 575


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: 788
Number of extensions: 37
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 552
Length of database: 594
Length adjustment: 36
Effective length of query: 516
Effective length of database: 558
Effective search space:   287928
Effective search space used:   287928
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