Alignments for a candidate for ilvD in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Dyella japonica UNC79MFTsu3.2

Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate N515DRAFT_0569 N515DRAFT_0569 dihydroxy-acid dehydratase

Query= metacyc::MONOMER-18815
         (557 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0569
          Length = 568

 Score =  454 bits (1168), Expect = e-132
 Identities = 245/552 (44%), Positives = 338/552 (61%), Gaps = 8/552 (1%)

Query: 6   RSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADAAIDAI 65
           RS  I  G  R+P R+M  A G       KP+V + +  S ++PCN  L+ LA+   + I
Sbjct: 2   RSDLIKTGADRAPARAMLRATGLDDGAIAKPLVAVVHTWSNVSPCNLNLRELAEQVAEGI 61

Query: 66  KASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVIGGCDK 125
           +A+   P  F T  ++DG++MGT GM+ SLISREVI D IE A  G  +D +VV+ GCDK
Sbjct: 62  RAAGGTPIEFNTIAVTDGIAMGTPGMRASLISREVITDSIELAVDGHCLDAMVVLCGCDK 121

Query: 126 NMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQEDFEGVE 185
            +P   +A+AR ++P + +YGGTI  G      +TI   FEAVG   AG++   +   VE
Sbjct: 122 TIPAAAMAMARLDIPAVALYGGTIAHGTHDAHPITIQQVFEAVGAHGAGKIDDAELAAVE 181

Query: 186 KNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLVEAIKQ 245
           ++ACP  G+CGG +TANTM+     LG+S +  + +      K  +A     ++++ +++
Sbjct: 182 RDACPGAGACGGQFTANTMAMVLTTLGLSPMGFNDIPATHPAKAAAARRCGELVMDCLRE 241

Query: 246 DIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRKVPVIC 305
              PR +I R S+ NA  ++ AT GSTNAVLH LAIA  A   WT++DFE   +  PVI 
Sbjct: 242 QRTPRALINRTSLRNAARMVAATAGSTNAVLHLLAIAREAGAPWTLEDFEPASKHTPVIA 301

Query: 306 NLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTPRAD-Q 364
           +L P G+Y A ++  AGG  +V + L+ AGML  D  T+TGR+L EE       PRA+ Q
Sbjct: 302 DLLPGGRYTAVEMFGAGGAARVAQELIAAGML-DDVPTVTGRSLFEE---AAAAPRAEQQ 357

Query: 365 DVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEAILAD 424
           DVILP+ + L   G  +IL GNLA EG + K+ G       G ARVFE E+ A  A+   
Sbjct: 358 DVILPVGQPLKPRGGYSILYGNLAPEGCILKLAGKGATHFEGTARVFESEEQAFAAVQQG 417

Query: 425 KINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMVVGHV 484
           +I  GD++V+R  GP GGPGM EML  T+A+IG+GLG+ V  ITDGRFSG T G +VGH+
Sbjct: 418 RIAKGDVIVIRNEGPAGGPGMREMLGVTAALIGRGLGDDVALITDGRFSGATHGFMVGHM 477

Query: 485 APEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVLAKFS 544
           APEA  GG IAL+++GD I IDA    L+    D +LA RR +W  PAP+ T G LAK++
Sbjct: 478 APEAVRGGPIALLRDGDRIRIDAG---LREIATDADLAERRQHWTPPAPKVTTGALAKYA 534

Query: 545 KLASTASKGAVT 556
           +L  +AS GA T
Sbjct: 535 RLVGSASDGANT 546


Lambda     K      H
   0.316    0.133    0.386 

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: 884
Number of extensions: 38
Number of successful extensions: 5
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: 568
Length adjustment: 36
Effective length of query: 521
Effective length of database: 532
Effective search space:   277172
Effective search space used:   277172
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 N515DRAFT_0569 N515DRAFT_0569 (dihydroxy-acid dehydratase)
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.30639.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   4.8e-191  621.9   4.5     6e-191  621.6   4.5    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0569  N515DRAFT_0569 dihydroxy-acid de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0569  N515DRAFT_0569 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  621.6   4.5    6e-191    6e-191       1     540 [.      14     545 ..      14     547 .. 0.99

  Alignments for each domain:
  == domain 1  score: 621.6 bits;  conditional E-value: 6e-191
                                    TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDG 66 
                                                  +ara+l+atGl d  + kP++avv +++++ P++++l++la++v+e+i+aaGg++ efntiav+DG
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0569  14 PARAMLRATGLDDGAIAKPLVAVVHTWSNVSPCNLNLRELAEQVAEGIRAAGGTPIEFNTIAVTDG 79 
                                                  579*************************************************************** PP

                                    TIGR00110  67 iamgheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpm 132
                                                  iamg+ Gm+ sL sre+i Ds+e  v++h+lDa+vv+  CDk +P + ma++rl+iPa++ +GG++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0569  80 IAMGTPGMRASLISREVITDSIELAVDGHCLDAMVVLCGCDKTIPAAAMAMARLDIPAVALYGGTI 145
                                                  ****************************************************************** PP

                                    TIGR00110 133 eagktklsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGls 198
                                                  + g    ++ i++ +vfeavg+  agk++++el ++er acP+ag+C+G ftan+ma++  +lGls
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0569 146 AHGTHD-AHPITIQQVFEAVGAHGAGKIDDAELAAVERDACPGAGACGGQFTANTMAMVLTTLGLS 210
                                                  ***999.8********************************************************** PP

                                    TIGR00110 199 lPgsstllatsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhlla 264
                                                    g   ++at+  k++ a++ g+ +++ ++++ +Pr +++++++ na  ++ a+ Gstn+vLhlla
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0569 211 PMGFNDIPATHPAKAAAARRCGELVMDCLREQRTPRALINRTSLRNAARMVAATAGSTNAVLHLLA 276
                                                  ****************************************************************** PP

                                    TIGR00110 265 iakeagvklslddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtG 330
                                                  ia+eag   +l+df+  s+++P++a+l P+g++  +++  aGG   v +el  +g+l +d+ tvtG
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0569 277 IAREAGAPWTLEDFEPASKHTPVIADLLPGGRYTAVEMFGAGGAARVAQELIAAGML-DDVPTVTG 341
                                                  ***************************************************999988.588***** PP

                                    TIGR00110 331 ktlaetlekvkvlrvdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvf 396
                                                  ++l e+++ ++   ++qdvi ++ +p+k  gg  +L+Gnla+eG++ k ag+    ++feG+a+vf
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0569 342 RSLFEEAAAAPRA-EQQDVILPVGQPLKPRGGYSILYGNLAPEGCILKLAGKGA--THFEGTARVF 404
                                                  *********9999.99***********************************998..********** PP

                                    TIGR00110 397 eseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtr 462
                                                  esee+a +a+ +g++ +Gdv+vir eGP GgPGmremL  t+al+g GLg++vaLitDGrfsG+t+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0569 405 ESEEQAFAAVQQGRIAKGDVIVIRNEGPAGGPGMREMLGVTAALIGRGLGDDVALITDGRFSGATH 470
                                                  ****************************************************************** PP

                                    TIGR00110 463 GlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkearevkgaLaky 528
                                                  G+++Gh++Pea+ gG+ial++dGD+i+iD+  r++     +++laerr++++++ ++ + gaLaky
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0569 471 GFMVGHMAPEAVRGGPIALLRDGDRIRIDAGLREIA---TDADLAERRQHWTPPAPKVTTGALAKY 533
                                                  *********************************997...6899*********************** PP

                                    TIGR00110 529 aklvssadkGav 540
                                                  a+lv sa++Ga 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0569 534 ARLVGSASDGAN 545
                                                  **********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (568 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.37
//
[ok]

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:

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