Alignments for a candidate for ilvD in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Desulfovibrio vulgaris Miyazaki F

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate 8501301 DvMF_2034 dihydroxy-acid dehydratase (RefSeq)

Query= metacyc::MONOMER-11919
         (549 letters)



>FitnessBrowser__Miya:8501301
          Length = 555

 Score =  575 bits (1481), Expect = e-168
 Identities = 290/555 (52%), Positives = 401/555 (72%), Gaps = 7/555 (1%)

Query: 1   MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60
           M+S  +  G+++APHRSLL   GLT ++ E+P +G+ N+  ++VPGH+HL  +AEAVK G
Sbjct: 1   MRSKKMTHGLEKAPHRSLLHALGLTREEIERPLVGVVNAANEVVPGHVHLHTIAEAVKAG 60

Query: 61  VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120
           V AAGG   EF  +A+CDG+AMNH+GM +SL SREI+AD++E MA AH  D LV +P CD
Sbjct: 61  VRAAGGTPMEFPAIAVCDGLAMNHEGMHFSLPSREIIADSIEIMATAHPFDALVFIPNCD 120

Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180
           K VPGMLMA  R+DIP+I+V+GGPML G     + DLI+V+E VG V  G+M+  EL+E+
Sbjct: 121 KSVPGMLMAMLRMDIPSIMVSGGPMLAGGTLAGRTDLISVFEAVGRVQRGDMTMAELDEM 180

Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240
              ACPG  SCAG+FTANTM C+ E +G++LPG  T  AV++ + ++A+ +G +++E+++
Sbjct: 181 TETACPGCGSCAGMFTANTMNCMAETMGLALPGNGTIPAVTAARVRLAKHAGMKVMELLE 240

Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300
           +N+ P  I++  A  NAV VD+ALGGSTNT LH+PA+  E  GL++ LD+FDE+SR  P+
Sbjct: 241 KNITPRSIVTPRAVANAVAVDMALGGSTNTVLHLPAVFGEA-GLDLTLDIFDEVSRKTPN 299

Query: 301 IASISPAGEHMMLDLDRAGGIPAVLK--TLEDHINRECVTCTGRTVQENIE--NVKVGHR 356
           +  +SPAG H + DL  AGGIPAV+   T +  ++   +T TG+T+ EN+   N +V + 
Sbjct: 300 LCKLSPAGHHHIQDLHAAGGIPAVMAELTRKGLVDTSVMTVTGKTLAENLAELNARVLNP 359

Query: 357 DVIRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIF 416
           DVIR  D+P  ++GG+AIL+G+LAP+G+VVKQ AVA +MMV E  A+VF+SE E   AI 
Sbjct: 360 DVIRSADAPYSAQGGIAILKGSLAPQGAVVKQSAVAPEMMVREAVARVFDSEGEAHAAIM 419

Query: 417 GGRIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTRGPCVG 475
           GG+I++GD I+IRYEGP+GGPGMREML+PT+AIAGMGL   VALITDGRFSGGTRG  +G
Sbjct: 420 GGKINKGDAIIIRYEGPRGGPGMREMLSPTAAIAGMGLGADVALITDGRFSGGTRGAAIG 479

Query: 476 HVSPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVKG-WLAR 534
           HVSPEA + G +  V +GD I IDIP+R+L++ +   E+  R ++ V   + V    L R
Sbjct: 480 HVSPEAADGGNIGLVREGDHILIDIPARRLDLLVDEAELAARRETFVPLEKPVTSPLLRR 539

Query: 535 YRKLAGSADTGAVLR 549
           Y +   SA TGA+ R
Sbjct: 540 YARQVTSAATGAMYR 554


Lambda     K      H
   0.319    0.136    0.397 

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: 992
Number of extensions: 59
Number of successful extensions: 4
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: 549
Length of database: 555
Length adjustment: 36
Effective length of query: 513
Effective length of database: 519
Effective search space:   266247
Effective search space used:   266247
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate 8501301 DvMF_2034 (dihydroxy-acid dehydratase (RefSeq))
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.24280.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   5.1e-235  767.0  10.3   5.8e-235  766.8  10.3    1.0  1  lcl|FitnessBrowser__Miya:8501301  DvMF_2034 dihydroxy-acid dehydra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501301  DvMF_2034 dihydroxy-acid dehydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  766.8  10.3  5.8e-235  5.8e-235       1     542 [.      14     554 ..      14     555 .] 0.99

  Alignments for each domain:
  == domain 1  score: 766.8 bits;  conditional E-value: 5.8e-235
                         TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmkys 77 
                                       ++r+ll+a+Gl+ e++e+P+++vvn+ +e+vPghvhl+ +a++vk++++aaGg+++ef  iav+DG+am+heGm++s
  lcl|FitnessBrowser__Miya:8501301  14 PHRSLLHALGLTREEIERPLVGVVNAANEVVPGHVHLHTIAEAVKAGVRAAGGTPMEFPAIAVCDGLAMNHEGMHFS 90 
                                       69*************************************************************************** PP

                         TIGR00110  78 LpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvdvfeavge 154
                                       LpsreiiaDs+e +++ah +Dalv i++CDk vPGmlma+lr++iP+i+vsGGpm ag t  + + dl++vfeavg+
  lcl|FitnessBrowser__Miya:8501301  91 LPSREIIADSIEIMATAHPFDALVFIPNCDKSVPGMLMAMLRMDIPSIMVSGGPMLAGGTL-AGRTDLISVFEAVGR 166
                                       **********************************************************998.5789*********** PP

                         TIGR00110 155 yaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkrivelvkkni 231
                                       ++ g+++ +el+e+ ++acP++gsC+G+ftan+m+c++e++Gl+lPg++t++a++a + +lak++g++++el++kni
  lcl|FitnessBrowser__Miya:8501301 167 VQRGDMTMAELDEMTETACPGCGSCAGMFTANTMNCMAETMGLALPGNGTIPAVTAARVRLAKHAGMKVMELLEKNI 243
                                       ***************************************************************************** PP

                         TIGR00110 232 kPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkviedlhraGGv 308
                                       +Pr+i+t +a+ na+++d+alGGstntvLhl+a+  eag++l+ld fd++srk+P l+kl+P+g++ i+dlh+aGG+
  lcl|FitnessBrowser__Miya:8501301 244 TPRSIVTPRAVANAVAVDMALGGSTNTVLHLPAVFGEAGLDLTLDIFDEVSRKTPNLCKLSPAGHHHIQDLHAAGGI 320
                                       ***************************************************************************** PP

                         TIGR00110 309 savlkeldkegllhkdaltvtGktlaetlekvkvlrvdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveed 385
                                       +av+ el+++gl+++ ++tvtGktlae+l++ + + ++ dvirs d p++++gg+a+LkG+la++Gavvk+++v+ +
  lcl|FitnessBrowser__Miya:8501301 321 PAVMAELTRKGLVDTSVMTVTGKTLAENLAELNARVLNPDVIRSADAPYSAQGGIAILKGSLAPQGAVVKQSAVAPE 397
                                       ***************************************************************************** PP

                         TIGR00110 386 ilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtr 462
                                       +++ e  a+vf+se ea +ai+ggk+++Gd ++iryeGP+GgPGmremL Pt+a++g+GLg +vaLitDGrfsGgtr
  lcl|FitnessBrowser__Miya:8501301 398 MMVREAVARVFDSEGEAHAAIMGGKINKGDAIIIRYEGPRGGPGMREMLSPTAAIAGMGLGADVALITDGRFSGGTR 474
                                       ***************************************************************************** PP

                         TIGR00110 463 GlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGa 539
                                       G +iGhvsPeaa gG+i+lv++GD+i iDi++r+ldl v+e+ela+rr++ ++ e+  ++ +L++ya+ v+sa +Ga
  lcl|FitnessBrowser__Miya:8501301 475 GAAIGHVSPEAADGGNIGLVREGDHILIDIPARRLDLLVDEAELAARRETFVPLEKPVTSPLLRRYARQVTSAATGA 551
                                       *******************************************************99******************** PP

                         TIGR00110 540 vld 542
                                       + +
  lcl|FitnessBrowser__Miya:8501301 552 MYR 554
                                       875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (555 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: 11.89
//
[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