Alignments for a candidate for ilvD in Malonomonas rubra DSM 5091

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Malonomonas rubra DSM 5091

Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_072905972.1 BUB13_RS04405 dihydroxy-acid dehydratase

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



>NCBI__GCF_900142125.1:WP_072905972.1
          Length = 567

 Score =  543 bits (1398), Expect = e-159
 Identities = 283/565 (50%), Positives = 386/565 (68%), Gaps = 14/565 (2%)

Query: 5   KRSQNIT------QGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLA 58
           +RS  IT        V R+  R+M  A+ +  EDF KP++ +A  ++  TPCN  ++ L 
Sbjct: 3   RRSNEITGDRNEGNWVERTAARTMLRAVRFSDEDFAKPLIALAVPYTNGTPCNDHIRELG 62

Query: 59  DAAIDAIKASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVV 118
           D     I+A+     +FGTP +SDG+SMGTE MKYSL+SREVIAD IE   +G  +DGV+
Sbjct: 63  DLLQAEIEAAGGKAIIFGTPVVSDGISMGTEAMKYSLVSREVIADSIELMTEGYRVDGVI 122

Query: 119 VIGGCDKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQ 178
            + GCDK +P  ++ +AR ++ G+ +YGG+I PG  KG++L IVSSFEA+G F+AG++ +
Sbjct: 123 TLSGCDKTIPAALMPIARNDLIGLTLYGGSILPGRHKGEELNIVSSFEAIGAFSAGKIDE 182

Query: 179 EDFEGVEKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQE------KVDSA 232
           +   G+E +ACP  GSCGGMYTANTM+S+ EALGMSL  SS+    D+       K   A
Sbjct: 183 KQLHGIECHACPGAGSCGGMYTANTMASAIEALGMSLPGSSSNMAVDEANNLSAGKRSDA 242

Query: 233 AESARVLVEAIKQDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTID 292
           A SAR ++  +KQ+I  R I+TRK+ ENA+ +  A GGSTNAVLH LA+A  A V  ++ 
Sbjct: 243 AASARAMIALLKQNISSRQIMTRKAFENALTVAWALGGSTNAVLHILALAKEAGVALSLT 302

Query: 293 DFERIRRKVPVICNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEE 352
           D   I R+VP++ N KP G+Y+  DLH  GG+P +MK LL AG LHGDCLT++G+T+AE 
Sbjct: 303 DIAEITRRVPLLGNFKPFGRYLMNDLHVIGGVPMLMKHLLDAGFLHGDCLTVSGKTIAEN 362

Query: 353 LENVPDTPRADQDVILPIEKALYAEG-HLAILKGNLAEEGAVAKITGLKNPVITGPARVF 411
           L + P  P + QDV+ P++      G H+ IL GNLAEEG V K +G     ++GPARVF
Sbjct: 363 LADAPALP-SGQDVLYPLDSPYAPAGTHIRILYGNLAEEGCVLKQSGKNLATMSGPARVF 421

Query: 412 EDEQSAMEAILADKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGR 471
           E E+ A+ AIL+ +I   DI+V+RY GPKGGPGM EML+P++A++G GLG+SV  ITDGR
Sbjct: 422 EREEDALTAILSGEIKPKDIVVIRYEGPKGGPGMREMLSPSAALMGAGLGDSVALITDGR 481

Query: 472 FSGGTWGMVVGHVAPEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQP 531
           FSGGT G+++GHV+PEA  GG IALV+EGD I ID  +  L L V   EL +RR +W   
Sbjct: 482 FSGGTHGIMIGHVSPEAQDGGNIALVREGDIIEIDLAREQLNLKVEPGELEQRRRDWLPQ 541

Query: 532 APRYTRGVLAKFSKLASTASKGAVT 556
             +Y RGVL+K+++L S+AS+GAVT
Sbjct: 542 ENKYQRGVLSKYARLVSSASQGAVT 566


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: 889
Number of extensions: 47
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: 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 WP_072905972.1 BUB13_RS04405 (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.32117.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-213  695.7   1.7   2.4e-213  695.5   1.7    1.0  1  lcl|NCBI__GCF_900142125.1:WP_072905972.1  BUB13_RS04405 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900142125.1:WP_072905972.1  BUB13_RS04405 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  695.5   1.7  2.4e-213  2.4e-213       2     541 ..      23     566 ..      22     567 .] 0.97

  Alignments for each domain:
  == domain 1  score: 695.5 bits;  conditional E-value: 2.4e-213
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               ar++l+a+ ++ded+ kP+ia++  yt+ +P++ h+++l++l ++eieaaGg+a  f+t  vsDGi+mg
  lcl|NCBI__GCF_900142125.1:WP_072905972.1  23 ARTMLRAVRFSDEDFAKPLIALAVPYTNGTPCNDHIRELGDLLQAEIEAAGGKAIIFGTPVVSDGISMG 91 
                                               79******************************************************************* PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               +e mkysL+sre+iaDs+e + ++ ++D+++++s CDk +P +lm  +r ++  +  +GG++ +g+ k 
  lcl|NCBI__GCF_900142125.1:WP_072905972.1  92 TEAMKYSLVSREVIADSIELMTEGYRVDGVITLSGCDKTIPAALMPIARNDLIGLTLYGGSILPGRHK- 159
                                               ********************************************************************. PP

                                 TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208
                                               +e++++v+ fea+g+ +agk++e++l+ ie +acP+agsC+G++tan+ma++ ealG+slPgss+ +a+
  lcl|NCBI__GCF_900142125.1:WP_072905972.1 160 GEELNIVSSFEAIGAFSAGKIDEKQLHGIECHACPGAGSCGGMYTANTMASAIEALGMSLPGSSSNMAV 228
                                               9****************************************************************9999 PP

                                 TIGR00110 209 s......aekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagv 271
                                               +      a k++ a  s++ ++ l+k+ni  r+i+t++afena+t+  alGGstn+vLh+la+akeagv
  lcl|NCBI__GCF_900142125.1:WP_072905972.1 229 DeannlsAGKRSDAAASARAMIALLKQNISSRQIMTRKAFENALTVAWALGGSTNAVLHILALAKEAGV 297
                                               622222145778888999*************************************************** PP

                                 TIGR00110 272 klslddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekv 340
                                                lsl d+ +++r+vPll+++kP g+++++dlh  GGv++++k+l  +g lh d+ltv+Gkt+ae+l+++
  lcl|NCBI__GCF_900142125.1:WP_072905972.1 298 ALSLTDIAEITRRVPLLGNFKPFGRYLMNDLHVIGGVPMLMKHLLDAGFLHGDCLTVSGKTIAENLADA 366
                                               ********************************************************************* PP

                                 TIGR00110 341 kvlrvdqdvirsldnpvkkeg.glavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailg 408
                                               + l+ +qdv+ +ld+p+   g ++++L+GnlaeeG+v k++g++    ++ Gpa+vfe ee+al ail+
  lcl|NCBI__GCF_900142125.1:WP_072905972.1 367 PALPSGQDVLYPLDSPYAPAGtHIRILYGNLAEEGCVLKQSGKNL--ATMSGPARVFEREEDALTAILS 433
                                               *****************977659*******************875..999******************* PP

                                 TIGR00110 409 gkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegG 477
                                               g++k  d+vviryeGPkGgPGmremL P++al+g+GLg++vaLitDGrfsGgt+G++iGhvsPea  gG
  lcl|NCBI__GCF_900142125.1:WP_072905972.1 434 GEIKPKDIVVIRYEGPKGGPGMREMLSPSAALMGAGLGDSVALITDGRFSGGTHGIMIGHVSPEAQDGG 502
                                               ********************************************************************* PP

                                 TIGR00110 478 aialvedGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541
                                               +ialv++GD+i+iD+ +++l+l+v+  el++rr+++ ++e+++++g+L+kya+lvssa++Gav+
  lcl|NCBI__GCF_900142125.1:WP_072905972.1 503 NIALVREGDIIEIDLAREQLNLKVEPGELEQRRRDWLPQENKYQRGVLSKYARLVSSASQGAVT 566
                                               **************************************************************97 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: 00:00:00.02
# Mc/sec: 12.26
//
[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