Alignments for a candidate for ilvD in Paraburkholderia phymatum STM815

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Paraburkholderia phymatum STM815

Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_012401602.1 BPHY_RS11300 dihydroxy-acid dehydratase

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



>NCBI__GCF_000020045.1:WP_012401602.1
          Length = 557

 Score = 1006 bits (2601), Expect = 0.0
 Identities = 494/556 (88%), Positives = 533/556 (95%)

Query: 1   MAFNKRSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADA 60
           M +N+RS+NITQGVARSPNRSMYYALGY+K DFDKPM+GIANGHSTITPCNAGLQRLADA
Sbjct: 1   MPYNRRSKNITQGVARSPNRSMYYALGYQKADFDKPMIGIANGHSTITPCNAGLQRLADA 60

Query: 61  AIDAIKASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVI 120
           A++A+K SDANPQ FGTPTISDGMSMGTEGMKYSL+SREVIADCIET  QGQWMDGVVVI
Sbjct: 61  AVEAVKRSDANPQTFGTPTISDGMSMGTEGMKYSLVSREVIADCIETCVQGQWMDGVVVI 120

Query: 121 GGCDKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQED 180
           GGCDKNMPGGMI LAR NVPGIYVYGGTIKPGNWKG DLTIVSSFEAVGEFTAGRMSQED
Sbjct: 121 GGCDKNMPGGMIGLARMNVPGIYVYGGTIKPGNWKGTDLTIVSSFEAVGEFTAGRMSQED 180

Query: 181 FEGVEKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV 240
           FEGVE+NACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV
Sbjct: 181 FEGVEQNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV 240

Query: 241 EAIKQDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRK 300
           EA+KQD+KPRDIIT+KSIENAVALIMATGGSTNAVLHYLAIAHAAEV+W+I+DFER+R+K
Sbjct: 241 EAVKQDLKPRDIITKKSIENAVALIMATGGSTNAVLHYLAIAHAAEVDWSIEDFERMRKK 300

Query: 301 VPVICNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTP 360
           VPVIC+LKPSG+YVATDLHKAGGIPQV+K+LL AG+LHGDC+TITG+T+AEEL++VP  P
Sbjct: 301 VPVICDLKPSGKYVATDLHKAGGIPQVLKLLLDAGLLHGDCITITGKTIAEELKDVPAKP 360

Query: 361 RADQDVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEA 420
           RADQ VI PI+KALY+EGHLAILKGNLAE+GAVAKITGLKNPVITGPARVF+DEQSAMEA
Sbjct: 361 RADQKVIYPIDKALYSEGHLAILKGNLAEDGAVAKITGLKNPVITGPARVFDDEQSAMEA 420

Query: 421 ILADKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMV 480
           ILAD+I AGD++VLRYLGP+GGPGMPEMLAPTSAIIGKGLGESVG ITDGRFSGGTWGMV
Sbjct: 421 ILADQIKAGDVVVLRYLGPQGGPGMPEMLAPTSAIIGKGLGESVGLITDGRFSGGTWGMV 480

Query: 481 VGHVAPEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVL 540
           VGHVAPEA+VGGTIALVQEGDSITIDAHKLLLQLNV D EL RRRA WKQPAPRYTRGVL
Sbjct: 481 VGHVAPEAFVGGTIALVQEGDSITIDAHKLLLQLNVDDGELQRRRAAWKQPAPRYTRGVL 540

Query: 541 AKFSKLASTASKGAVT 556
           AKF+ LA  A+KGAVT
Sbjct: 541 AKFAALAKPANKGAVT 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: 1214
Number of extensions: 40
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 WP_012401602.1 BPHY_RS11300 (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.8834.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-226  739.2   3.5   1.6e-226  739.0   3.5    1.0  1  lcl|NCBI__GCF_000020045.1:WP_012401602.1  BPHY_RS11300 dihydroxy-acid dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020045.1:WP_012401602.1  BPHY_RS11300 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  739.0   3.5  1.6e-226  1.6e-226       1     541 [.      18     556 ..      18     557 .] 0.99

  Alignments for each domain:
  == domain 1  score: 739.0 bits;  conditional E-value: 1.6e-226
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++r++++a+G++++d++kP+i+++n++++i+P++  l+ la+++ e+++++ + ++ f+t ++sDG++m
  lcl|NCBI__GCF_000020045.1:WP_012401602.1  18 PNRSMYYALGYQKADFDKPMIGIANGHSTITPCNAGLQRLADAAVEAVKRSDANPQTFGTPTISDGMSM 86 
                                               68******************************************************************* PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               g+eGmkysL+sre+iaD +et v+++++D++vvi+ CDk++PG +++ +r+n+P i v+GG++++g+ k
  lcl|NCBI__GCF_000020045.1:WP_012401602.1  87 GTEGMKYSLVSREVIADCIETCVQGQWMDGVVVIGGCDKNMPGGMIGLARMNVPGIYVYGGTIKPGNWK 155
                                               ********************************************************************* PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                + ++++v+ feavge +ag++s+e+ e +e++acP++gsC+G++tan+m++ +ealG+sl +sst++ 
  lcl|NCBI__GCF_000020045.1:WP_012401602.1 156 -GTDLTIVSSFEAVGEFTAGRMSQEDFEGVEQNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMAN 223
                                               .9******************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                                ++ek ++a +s++ +ve+vk+++kPrdi+tk+++ena++l++a+GGstn+vLh laia+ a+v+ s++
  lcl|NCBI__GCF_000020045.1:WP_012401602.1 224 PDQEKVDSAAESARVLVEAVKQDLKPRDIITKKSIENAVALIMATGGSTNAVLHYLAIAHAAEVDWSIE 292
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr. 344
                                               df+r+++kvP++++lkPsgk+v +dlh+aGG+++vlk l  +gllh d++t+tGkt+ae+l++v+ ++ 
  lcl|NCBI__GCF_000020045.1:WP_012401602.1 293 DFERMRKKVPVICDLKPSGKYVATDLHKAGGIPQVLKLLLDAGLLHGDCITITGKTIAEELKDVPAKPr 361
                                               ****************************************************************99864 PP

                                 TIGR00110 345 vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvke 413
                                               +dq+vi ++d+++++eg+la+LkGnlae+Gav+ki+g ++   +++Gpa+vf++e+ a+eail+ ++k+
  lcl|NCBI__GCF_000020045.1:WP_012401602.1 362 ADQKVIYPIDKALYSEGHLAILKGNLAEDGAVAKITGLKN--PVITGPARVFDDEQSAMEAILADQIKA 428
                                               7999************************************..999************************ PP

                                 TIGR00110 414 GdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialv 482
                                               Gdvvv+ry GP+GgPGm+emLaPtsa++g GLg++v+LitDGrfsGgt G+++Ghv+Pea +gG+ialv
  lcl|NCBI__GCF_000020045.1:WP_012401602.1 429 GDVVVLRYLGPQGGPGMPEMLAPTSAIIGKGLGESVGLITDGRFSGGTWGMVVGHVAPEAFVGGTIALV 497
                                               ********************************************************************* PP

                                 TIGR00110 483 edGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541
                                               ++GD i+iD+++  l+l+v++ el++rra++k++ +r+++g+Lak+a l++ a+kGav+
  lcl|NCBI__GCF_000020045.1:WP_012401602.1 498 QEGDSITIDAHKLLLQLNVDDGELQRRRAAWKQPAPRYTRGVLAKFAALAKPANKGAVT 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.91
//
[ok]

This GapMind analysis is from Apr 10 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