Alignments for a candidate for ilvD in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Pseudomonas fluorescens GW456-L13

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate PfGW456L13_1889 Phosphogluconate dehydratase (EC 4.2.1.12)

Query= curated2:C4Z566
         (557 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889
          Length = 608

 Score =  258 bits (659), Expect = 5e-73
 Identities = 183/518 (35%), Positives = 264/518 (50%), Gaps = 42/518 (8%)

Query: 29  MKKPMIGIVSSYNEIVPGHMNIDKIVNAVKLGVAE-------AGGVPVVFPAIAVCDGIA 81
           M    I IVSSYN+++  H   +     +K  + E       AGG P      A+CDG+ 
Sbjct: 63  MNSANIAIVSSYNDMLSAHQPYEVFPELIKKALREIGSVGQFAGGTP------AMCDGVT 116

Query: 82  MGHVGMKYSLVTRDLIADSTECMAIAHQFDGLVMVPNCDKNVPGLLMAAARL-NLPTVFV 140
            G  GM+ SL +R++IA ST      + FDG +++  CDK VPGL+M A R  +LP +FV
Sbjct: 117 QGEPGMELSLPSREVIALSTAVALSHNMFDGALLLGICDKIVPGLMMGALRFGHLPMIFV 176

Query: 141 SGGPMLAGHVKGKKRSLSSMFEAVGSYAAGTMTEEDVLEFEEKVCPTCGSCSGMYTANSM 200
            GGPM++G    +K  +         YA G  T E++LE E K   + G+C+   TAN+ 
Sbjct: 177 PGGPMVSGISNKQKADVRQ------KYAEGKATREELLESEMKSYHSPGTCTFYGTANTN 230

Query: 201 NCLTEALGMGLRGNGTIPAVYSERIKLAKHAGMAVMDMVNKG---ITARDIITKDSIMNA 257
             L E +G+ L G   +      R  L + A   V  +  +    +   +I+ + S++N+
Sbjct: 231 QLLMEVMGLHLPGASFVNPNTPLRDALTREAAHQVTRLTKQNGDFMPIGEIVDERSLVNS 290

Query: 258 LTVDMALGCSTNSMLHLPAIAHEIGFDFDIKFANPISEKTPNLCHLAPAGPTYMEDLNEA 317
           +    A G STN  LH+PAIA   G     +    +SE  P L H+ P G   +     A
Sbjct: 291 IVALHATGGSTNHTLHMPAIAMAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAA 350

Query: 318 GGVYAVMKELADIGLLNTDCLTVSGKTIGECIATAY--------------NRDPEVIRTV 363
           GG+  +++EL + GLL+ +  TV G  +       +              + D  ++R V
Sbjct: 351 GGMSFLIRELLEAGLLHENVNTVMGHGLSRYTQEPFLDNGQLVWREGVTDSLDESILRPV 410

Query: 364 DNAYSKTGGLAVLSGNLAPDGSVVKRSAVVPEMLVHEGPARVFDSEEDAIAAIKGGKIVE 423
             A+S  GGL V+ GNL     V+K SAV  E  + E PA VF  ++D   A K G + +
Sbjct: 411 ARAFSAEGGLRVMEGNLG--RGVMKVSAVAVENQIVEAPAMVFQDQQDLADAFKAGLLEK 468

Query: 424 GDVVVIRYEGPKGGPGMREMLNPTSAIAGM-GLGSSVALITDGRFSGAS-RGASIGHVSP 481
             V V+R++GP+   GM E+   T  +  +   G  VAL+TDGR SGAS +  +  HVSP
Sbjct: 469 DFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSP 527

Query: 482 EAAVGGPIALVEEGDIISIDIPGLKLELKVSDEELAAR 519
           EA VGG +A V+EGDII +D     LELKV  EE AAR
Sbjct: 528 EAYVGGALARVQEGDIIRVDGVKGTLELKVDAEEFAAR 565


Lambda     K      H
   0.317    0.134    0.385 

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: 873
Number of extensions: 55
Number of successful extensions: 10
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: 557
Length of database: 608
Length adjustment: 36
Effective length of query: 521
Effective length of database: 572
Effective search space:   298012
Effective search space used:   298012
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 (21.6 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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for Amino acid biosynthesis