Alignments for a candidate for ilvD in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Acidovorax sp. GW101-3H11

Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate Ac3H11_954 Dihydroxy-acid dehydratase (EC 4.2.1.9)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_954
          Length = 567

 Score =  875 bits (2260), Expect = 0.0
 Identities = 427/554 (77%), Positives = 491/554 (88%)

Query: 4   NKRSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADAAID 63
           N+RS NITQG +R+PNRSMYYA+GY++ DF KPMVG+ANGHSTITPCN+GLQ+LADAAI 
Sbjct: 12  NRRSANITQGKSRAPNRSMYYAMGYEEGDFVKPMVGVANGHSTITPCNSGLQKLADAAIA 71

Query: 64  AIKASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVIGGC 123
            I+ +  N QVFGTPTISDGM+MGTEGMKYSL+SREVI+DCIET   GQWMDGV+V+GGC
Sbjct: 72  GIEEAGGNAQVFGTPTISDGMAMGTEGMKYSLVSREVISDCIETCVGGQWMDGVLVVGGC 131

Query: 124 DKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQEDFEG 183
           DKNMPGG++ + R NVP IYVYGGTI PG+++GKDL IVS FEAVGE  AG++S  D + 
Sbjct: 132 DKNMPGGLMGMLRANVPAIYVYGGTILPGHYQGKDLNIVSVFEAVGENAAGKLSDFDLKE 191

Query: 184 VEKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLVEAI 243
           +EK A P TGSCGGMYTANTMSS+FEALG+SL YSSTMANP  EK++SA ESA+VL+EAI
Sbjct: 192 IEKRAIPGTGSCGGMYTANTMSSAFEALGISLPYSSTMANPHDEKMNSAKESAKVLIEAI 251

Query: 244 KQDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRKVPV 303
           K+DIKPRDI+T+KSIENAVA+IMATGGSTNAVLH+LAIAHAA VEW+IDDFER+R K PV
Sbjct: 252 KKDIKPRDIVTKKSIENAVAVIMATGGSTNAVLHFLAIAHAAGVEWSIDDFERVRVKTPV 311

Query: 304 ICNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTPRAD 363
           +C+LKPSG+Y+A DLH+AGGIPQVMK+LL AG+LHGDCLTI G+T+AE L++VPD PRAD
Sbjct: 312 LCDLKPSGKYLAVDLHRAGGIPQVMKVLLNAGLLHGDCLTIEGKTVAEVLKDVPDQPRAD 371

Query: 364 QDVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEAILA 423
           QDVI PI   +YA+GHLAILKGNL+ EGAVAKITGLKNPVITGPARVFEDEQSA+EAILA
Sbjct: 372 QDVIRPINNPMYAQGHLAILKGNLSPEGAVAKITGLKNPVITGPARVFEDEQSALEAILA 431

Query: 424 DKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMVVGH 483
            KI AGD++VLRYLGPKGGPGMPEMLAPT A+IG GLGESVG ITDGRFSGGTWGMVVGH
Sbjct: 432 GKIKAGDVMVLRYLGPKGGPGMPEMLAPTGALIGAGLGESVGLITDGRFSGGTWGMVVGH 491

Query: 484 VAPEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVLAKF 543
           VAPEA  GGTIA V EGDSITIDA +LLL+LNV++EE+ARRRA W  PAPRYTRGV AKF
Sbjct: 492 VAPEAAAGGTIAFVHEGDSITIDARQLLLELNVSEEEIARRRAAWTAPAPRYTRGVQAKF 551

Query: 544 SKLASTASKGAVTD 557
           +  AS+ASKGAV D
Sbjct: 552 AFNASSASKGAVLD 565


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: 1137
Number of extensions: 42
Number of successful extensions: 1
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: 567
Length adjustment: 36
Effective length of query: 521
Effective length of database: 531
Effective search space:   276651
Effective search space used:   276651
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 Ac3H11_954 (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.31168.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   1.1e-229  749.4   5.9   1.3e-229  749.2   6.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954  Dihydroxy-acid dehydratase (EC 4


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954  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 !  749.2   6.0  1.3e-229  1.3e-229       1     542 [.      26     565 ..      26     566 .. 0.99

  Alignments for each domain:
  == domain 1  score: 749.2 bits;  conditional E-value: 1.3e-229
                                       TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiav 63 
                                                     ++r++++a+G+++ d+ kP+++v+n++++i+P++  l++la+++ ++ie+aGg a+ f+t ++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954  26 PNRSMYYAMGYEEGDFVKPMVGVANGHSTITPCNSGLQKLADAAIAGIEEAGGNAQVFGTPTI 88 
                                                     68************************************************************* PP

                                       TIGR00110  64 sDGiamgheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaiv 126
                                                     sDG+amg+eGmkysL+sre+i+D +et v ++++D+++v++ CDk++PG lm++lr n+Pai 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954  89 SDGMAMGTEGMKYSLVSREVISDCIETCVGGQWMDGVLVVGGCDKNMPGGLMGMLRANVPAIY 151
                                                     *************************************************************** PP

                                       TIGR00110 127 vsGGpmeagktklsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansma 189
                                                     v+GG++ +g+++ ++++++v+vfeavge aagkls+ +l+eie+ a P++gsC+G++tan+m+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954 152 VYGGTILPGHYQ-GKDLNIVSVFEAVGENAAGKLSDFDLKEIEKRAIPGTGSCGGMYTANTMS 213
                                                     ************.9************************************************* PP

                                       TIGR00110 190 cltealGlslPgsstllatsaekkelakksgkrivelvkknikPrdiltkeafenaitldlal 252
                                                     +++ealG+slP+sst++  + ek+++ak+s+k ++e++kk+ikPrdi+tk+++ena+++++a+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954 214 SAFEALGISLPYSSTMANPHDEKMNSAKESAKVLIEAIKKDIKPRDIVTKKSIENAVAVIMAT 276
                                                     *************************************************************** PP

                                       TIGR00110 253 GGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkel 315
                                                     GGstn+vLh laia+ agv+ s+ddf+r++ k+P+l++lkPsgk++ +dlhraGG+++v+k+l
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954 277 GGSTNAVLHFLAIAHAAGVEWSIDDFERVRVKTPVLCDLKPSGKYLAVDLHRAGGIPQVMKVL 339
                                                     *************************************************************** PP

                                       TIGR00110 316 dkegllhkdaltvtGktlaetlekvkvlr.vdqdvirsldnpvkkegglavLkGnlaeeGavv 377
                                                      ++gllh d+lt+ Gkt+ae+l++v+ ++ +dqdvir+++np++++g+la+LkGnl++eGav+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954 340 LNAGLLHGDCLTIEGKTVAEVLKDVPDQPrADQDVIRPINNPMYAQGHLAILKGNLSPEGAVA 402
                                                     *************************9886489******************************* PP

                                       TIGR00110 378 kiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsal 440
                                                     ki+g ++   +++Gpa+vfe+e+ aleail+gk+k+Gdv+v+ry GPkGgPGm+emLaPt al
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954 403 KITGLKN--PVITGPARVFEDEQSALEAILAGKIKAGDVMVLRYLGPKGGPGMPEMLAPTGAL 463
                                                     *******..999*************************************************** PP

                                       TIGR00110 441 vglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevse 503
                                                     +g+GLg++v+LitDGrfsGgt G+++Ghv+Peaa+gG+ia+v++GD i+iD+ +  l+l+vse
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954 464 IGAGLGESVGLITDGRFSGGTWGMVVGHVAPEAAAGGTIAFVHEGDSITIDARQLLLELNVSE 526
                                                     *************************************************************** PP

                                       TIGR00110 504 eelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                                     ee+a+rra+++++ +r+++g+ ak+a  +ssa+kGavld
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954 527 EEIARRRAAWTAPAPRYTRGVQAKFAFNASSASKGAVLD 565
                                                     *************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (567 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: 00:00:00.04
# Mc/sec: 6.42
//
[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