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 (EC 4.2.1.9) (characterized)
to candidate PfGW456L13_3725 Dihydroxy-acid dehydratase (EC 4.2.1.9)

Query= BRENDA::A0A481UJA7
         (614 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725
          Length = 560

 Score =  588 bits (1516), Expect = e-172
 Identities = 308/556 (55%), Positives = 391/556 (70%), Gaps = 4/556 (0%)

Query: 59  LNKYSSRITEPKSQGGSQAILHGVGLSDEDLNKPQIGISSVWYEGNTCNMHLLRLSEAVK 118
           L KYSS++ +      ++A+L  VG +D D  KPQIGI+S W     CNMH+ +L+   +
Sbjct: 7   LRKYSSQVIDGVEAAPARAMLRAVGFTDADFTKPQIGIASTWAMVTPCNMHIDKLALEAE 66

Query: 119 EGVKEAGMVGFRFNTIGVSDAISMGTRGMCYSLQSRDLIADSIETVMSAQWYDGNISIPG 178
           +G   AG  G  FNTI +SD I+ GT GM YSL SR++IADSIE V   + +DG ++I G
Sbjct: 67  KGANAAGAKGVIFNTITISDGIANGTEGMKYSLVSREVIADSIEVVTGCEGFDGLVTIGG 126

Query: 179 CDKNMPGTIMAMGRLNRPSIMVYGGTIKPGHYNGHSYDIISAFQAYGEYVNGSISDEDRK 238
           CDKNMPG ++ M RLNRPSI VYGGTI+PG   GH+ DIIS F+A G++  G IS+   K
Sbjct: 127 CDKNMPGCLIGMARLNRPSIFVYGGTIQPGA--GHT-DIISVFEAVGQHARGDISEIQVK 183

Query: 239 NVVHNSCPGAGACGGMYTANTMASAIEAMGMCLPYSSSIPAENPLKLDECRLAGKYLLEL 298
            +   + PG G+CGGMYTANTMASAIEA+GM LP SSS  A    K  +   AG+ ++EL
Sbjct: 184 QIEEVAIPGPGSCGGMYTANTMASAIEALGMSLPGSSSQDAIGADKASDSFRAGQQVMEL 243

Query: 299 LKMDLKPQNIITPQSLRNAMVVVMALGGSTNAVLHLIPIARSVGLELTLEDFQKVSDEVP 358
           LK+DLKP++I+T ++  NA+ VV+AL GSTNAVLHL+ +A +V +ELTL+DF ++    P
Sbjct: 244 LKLDLKPRDIMTRKAFENAIRVVIALAGSTNAVLHLLAMANAVDVELTLDDFVELGKVSP 303

Query: 359 FLADLKPSGKYVMEDVHKIGGTPAVLRYLLEHGFLDGDCLTVTGKTLAENVQNCPPLSEG 418
            +ADL+PSGKY+M ++  IGG   +++ +L+ G L GD LTVTG+TLAEN+ + P    G
Sbjct: 304 VVADLRPSGKYMMSELVAIGGIQPLMKRMLDAGMLHGDVLTVTGQTLAENLASVPDYPAG 363

Query: 419 QDIIRPLENPIKKTGHIQILQGNLAPEGSVAKITGKEGLYFSGPALVFEGEEAMLAAISE 478
           QD+IRP + PIKK  H+ IL+GNL+P G+VAKITGKEGL F G A V+ GEE  LA I  
Sbjct: 364 QDVIRPFDQPIKKDSHLVILRGNLSPTGAVAKITGKEGLRFEGTARVYHGEEGALAGILN 423

Query: 479 NPMNFKGKVVVIRGEGPKGGPGMPEMLTPTSAIMGAGLGKDCALLTDGRFSGGSHGFVVG 538
             +   G+V+VIR EGPKGGPGM EML+PTSA+MG GLGK+ AL+TDGRFSGGSHGFVVG
Sbjct: 424 GEVQ-PGEVIVIRYEGPKGGPGMREMLSPTSAVMGKGLGKEVALITDGRFSGGSHGFVVG 482

Query: 539 HICPEAQEGGPIGLVRNGDIIRIDVRERRIDVDVTDQEMEERRKNWTPPPYKATCGVLYK 598
           HI PEA EGGPI LV NGD I ID   R I VDV+D  + ER+  W  P  K   GVL K
Sbjct: 483 HITPEAFEGGPIALVENGDRIIIDAETRLITVDVSDAVLAERKSRWVRPESKYKRGVLAK 542

Query: 599 YIKNVQSASRGCVTDE 614
           Y K V SAS G VTD+
Sbjct: 543 YAKTVSSASEGAVTDK 558


Lambda     K      H
   0.316    0.135    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: 1003
Number of extensions: 43
Number of successful extensions: 3
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: 614
Length of database: 560
Length adjustment: 37
Effective length of query: 577
Effective length of database: 523
Effective search space:   301771
Effective search space used:   301771
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)

Align candidate PfGW456L13_3725 (Dihydroxy-acid dehydratase (EC 4.2.1.9))
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00110.hmm
# target sequence database:        /tmp/gapView.15442.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00110  [M=543]
Accession:   TIGR00110
Description: ilvD: dihydroxy-acid dehydratase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                               Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   7.8e-226  736.7   8.1     9e-226  736.5   8.1    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725  Dihydroxy-acid dehydratase (EC 4


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725  Dihydroxy-acid dehydratase (EC 4.2.1.9)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  736.5   8.1    9e-226    9e-226       1     542 [.      22     557 ..      22     558 .. 0.99

  Alignments for each domain:
  == domain 1  score: 736.5 bits;  conditional E-value: 9e-226
                                               TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgva 55 
                                                             +ara+l+a+G++d+d++kP+i++++++  ++P+++h+++la  ++++ +aaG++ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725  22 PARAMLRAVGFTDADFTKPQIGIASTWAMVTPCNMHIDKLALEAEKGANAAGAKG 76 
                                                             579**************************************************** PP

                                               TIGR00110  56 kefntiavsDGiamgheGmkysLpsreiiaDsvetvvkahalDalvvissCDkiv 110
                                                             + fnti++sDGia g+eGmkysL+sre+iaDs+e v   + +D+lv+i+ CDk++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725  77 VIFNTITISDGIANGTEGMKYSLVSREVIADSIEVVTGCEGFDGLVTIGGCDKNM 131
                                                             ******************************************************* PP

                                               TIGR00110 111 PGmlmaalrlniPaivvsGGpmeagktklsekidlvdvfeavgeyaagklseeel 165
                                                             PG l++++rln+P+i+v+GG++++g  +     d+++vfeavg+ a g++se ++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 132 PGCLIGMARLNRPSIFVYGGTIQPGAGH----TDIISVFEAVGQHARGDISEIQV 182
                                                             *************************887....699******************** PP

                                               TIGR00110 166 eeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksg 220
                                                             ++ie++a P++gsC+G++tan+ma++ ealG+slPgss+  a+ a+k++   ++g
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 183 KQIEEVAIPGPGSCGGMYTANTMASAIEALGMSLPGSSSQDAIGADKASDSFRAG 237
                                                             ******************************************************* PP

                                               TIGR00110 221 krivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsl 275
                                                             ++++el+k ++kPrdi+t++afenai +++al Gstn+vLhlla+a+ ++v+l+l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 238 QQVMELLKLDLKPRDIMTRKAFENAIRVVIALAGSTNAVLHLLAMANAVDVELTL 292
                                                             ******************************************************* PP

                                               TIGR00110 276 ddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtG 330
                                                             ddf +l +  P++a+l+Psgk+++ +l + GG++ ++k +  +g+lh d+ltvtG
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 293 DDFVELGKVSPVVADLRPSGKYMMSELVAIGGIQPLMKRMLDAGMLHGDVLTVTG 347
                                                             ******************************************************* PP

                                               TIGR00110 331 ktlaetlekvkvlrvdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveed 385
                                                             +tlae+l++v+  +++qdvir+ d+p+kk+++l +L+Gnl++ Gav+ki+g+e  
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 348 QTLAENLASVPDYPAGQDVIRPFDQPIKKDSHLVILRGNLSPTGAVAKITGKEG- 401
                                                             ******************************************************. PP

                                               TIGR00110 386 ilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsal 440
                                                              l+feG+a+v++ ee al++il+g+v+ G+v+viryeGPkGgPGmremL Ptsa+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 402 -LRFEGTARVYHGEEGALAGILNGEVQPGEVIVIRYEGPKGGPGMREMLSPTSAV 455
                                                             .****************************************************** PP

                                               TIGR00110 441 vglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienr 495
                                                             +g GLgk+vaLitDGrfsGg++G+++Gh++Pea egG+ialve+GD+i+iD+e r
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 456 MGKGLGKEVALITDGRFSGGSHGFVVGHITPEAFEGGPIALVENGDRIIIDAETR 510
                                                             ******************************************************* PP

                                               TIGR00110 496 kldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                                              + ++vs++ laer+ +++++e ++++g+Lakyak vssa++Gav+d
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 511 LITVDVSDAVLAERKSRWVRPESKYKRGVLAKYAKTVSSASEGAVTD 557
                                                             *********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (560 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 12.74
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
the source code
instructions for running GapMind on your computer
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