Alignments for a candidate for ilvD in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Burkholderia phytofirmans PsJN

Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate BPHYT_RS04815 BPHYT_RS04815 dihydroxy-acid dehydratase

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



>FitnessBrowser__BFirm:BPHYT_RS04815
          Length = 557

 Score =  989 bits (2557), Expect = 0.0
 Identities = 481/556 (86%), Positives = 528/556 (94%)

Query: 1   MAFNKRSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADA 60
           MA+N+RS+NITQGVARSPNRSMYYALGY+K DFDKPM+GIANGHSTITPCNAGLQRLADA
Sbjct: 1   MAYNRRSKNITQGVARSPNRSMYYALGYEKADFDKPMIGIANGHSTITPCNAGLQRLADA 60

Query: 61  AIDAIKASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVI 120
           A+ AIK +DANPQ+FGTPTISDGMSMGTEGMKYSL+SREVI+DCIET  QGQWMDGVVVI
Sbjct: 61  AVAAIKGADANPQIFGTPTISDGMSMGTEGMKYSLVSREVISDCIETCVQGQWMDGVVVI 120

Query: 121 GGCDKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQED 180
           GGCDKNMPGGMI + RTNVP IYVYGGTI+PGNWKG DLTIVSSFEAVGEFTAGRMSQED
Sbjct: 121 GGCDKNMPGGMIGMLRTNVPSIYVYGGTIRPGNWKGTDLTIVSSFEAVGEFTAGRMSQED 180

Query: 181 FEGVEKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV 240
           F+G+E+NACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV
Sbjct: 181 FDGIEQNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV 240

Query: 241 EAIKQDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRK 300
           E++K+D+KPRDI+T+KSIENAVA+IMATGGSTNAVLH+LAIAHAAEVEW+IDDFER+R+K
Sbjct: 241 ESVKKDLKPRDIVTKKSIENAVAVIMATGGSTNAVLHFLAIAHAAEVEWSIDDFERMRKK 300

Query: 301 VPVICNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTP 360
           VPVICNLKPSGQ+VATDLHKAGGIPQVMKILL AG+LHGDC+TITGRT+AEEL++VP  P
Sbjct: 301 VPVICNLKPSGQFVATDLHKAGGIPQVMKILLDAGLLHGDCITITGRTIAEELKDVPGKP 360

Query: 361 RADQDVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEA 420
           RADQ VI PI++ALY EGHLAILKGNLA +GAVAKITGLKNPVITGPARVF+DEQSA+EA
Sbjct: 361 RADQQVIFPIDQALYKEGHLAILKGNLAVDGAVAKITGLKNPVITGPARVFDDEQSALEA 420

Query: 421 ILADKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMV 480
           ILADKI AGD++VLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVG ITDGRFSGGTWGMV
Sbjct: 421 ILADKIVAGDVVVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGLITDGRFSGGTWGMV 480

Query: 481 VGHVAPEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVL 540
           VGHVAPEA+VGGTIA VQEGDSITIDAHKLLLQLN+ + EL RRRA W+QP PRYTRGV+
Sbjct: 481 VGHVAPEAFVGGTIAFVQEGDSITIDAHKLLLQLNIDNAELERRRAAWQQPKPRYTRGVM 540

Query: 541 AKFSKLASTASKGAVT 556
           AK+  LA  A+KGA+T
Sbjct: 541 AKYFALAQPANKGAIT 556


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: 1169
Number of extensions: 43
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: 557
Length adjustment: 36
Effective length of query: 521
Effective length of database: 521
Effective search space:   271441
Effective search space used:   271441
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 BPHYT_RS04815 BPHYT_RS04815 (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.2174.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
     9e-225  733.2   3.7     1e-224  733.0   3.7    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS04815  BPHYT_RS04815 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS04815  BPHYT_RS04815 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  733.0   3.7    1e-224    1e-224       1     541 [.      18     556 ..      18     557 .] 0.99

  Alignments for each domain:
  == domain 1  score: 733.0 bits;  conditional E-value: 1e-224
                                TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                              ++r++++a+G++++d++kP+i+++n++++i+P++  l+ la+++ ++i+ a + ++ f+t ++sDG++mg
  lcl|FitnessBrowser__BFirm:BPHYT_RS04815  18 PNRSMYYALGYEKADFDKPMIGIANGHSTITPCNAGLQRLADAAVAAIKGADANPQIFGTPTISDGMSMG 87 
                                              68******************************************************************** PP

                                TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkls 140
                                              +eGmkysL+sre+i+D +et v+++++D++vvi+ CDk++PG ++++lr+n+P+i v+GG++ +g+ k +
  lcl|FitnessBrowser__BFirm:BPHYT_RS04815  88 TEGMKYSLVSREVISDCIETCVQGQWMDGVVVIGGCDKNMPGGMIGMLRTNVPSIYVYGGTIRPGNWK-G 156
                                              ********************************************************************.9 PP

                                TIGR00110 141 ekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsa 210
                                               ++++v+ feavge +ag++s+e+ + ie++acP++gsC+G++tan+m++ +ealG+sl +sst++  ++
  lcl|FitnessBrowser__BFirm:BPHYT_RS04815 157 TDLTIVSSFEAVGEFTAGRMSQEDFDGIEQNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQ 226
                                              ********************************************************************** PP

                                TIGR00110 211 ekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdr 280
                                              ek ++a +s++ +ve vkk++kPrdi+tk+++ena+++++a+GGstn+vLh laia+ a+v+ s+ddf+r
  lcl|FitnessBrowser__BFirm:BPHYT_RS04815 227 EKVDSAAESARVLVESVKKDLKPRDIVTKKSIENAVAVIMATGGSTNAVLHFLAIAHAAEVEWSIDDFER 296
                                              ********************************************************************** PP

                                TIGR00110 281 lsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr.vdqdv 349
                                              +++kvP++++lkPsg+ v +dlh+aGG+++v+k l  +gllh d++t+tG+t+ae+l++v+ ++ +dq+v
  lcl|FitnessBrowser__BFirm:BPHYT_RS04815 297 MRKKVPVICNLKPSGQFVATDLHKAGGIPQVMKILLDAGLLHGDCITITGRTIAEELKDVPGKPrADQQV 366
                                              ************************************************************988638999* PP

                                TIGR00110 350 irsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvvi 419
                                              i ++d++++keg+la+LkGnla +Gav+ki+g ++   +++Gpa+vf++e+ aleail+ k+ +Gdvvv+
  lcl|FitnessBrowser__BFirm:BPHYT_RS04815 367 IFPIDQALYKEGHLAILKGNLAVDGAVAKITGLKN--PVITGPARVFDDEQSALEAILADKIVAGDVVVL 434
                                              ***********************************..999****************************** PP

                                TIGR00110 420 ryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkik 489
                                              ry GPkGgPGm+emLaPtsa++g GLg++v+LitDGrfsGgt G+++Ghv+Pea +gG+ia+v++GD i+
  lcl|FitnessBrowser__BFirm:BPHYT_RS04815 435 RYLGPKGGPGMPEMLAPTSAIIGKGLGESVGLITDGRFSGGTWGMVVGHVAPEAFVGGTIAFVQEGDSIT 504
                                              ********************************************************************** PP

                                TIGR00110 490 iDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541
                                              iD+++  l+l+++++el++rra+++++++r+++g++aky  l++ a+kGa++
  lcl|FitnessBrowser__BFirm:BPHYT_RS04815 505 IDAHKLLLQLNIDNAELERRRAAWQQPKPRYTRGVMAKYFALAQPANKGAIT 556
                                              **************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (557 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: 00:00:00.03
# Mc/sec: 9.92
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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