Alignments for a candidate for ilvD in Desulfuromusa kysingii DSM 7343

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Desulfuromusa kysingii DSM 7343

Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_092348740.1 BLU87_RS11915 dihydroxy-acid dehydratase

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



>NCBI__GCF_900107645.1:WP_092348740.1
          Length = 570

 Score =  545 bits (1404), Expect = e-159
 Identities = 276/550 (50%), Positives = 380/550 (69%), Gaps = 8/550 (1%)

Query: 14  VARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADAAIDAIKASDANPQ 73
           V R+ +R+M  A+ + +EDF KP++ +A  ++  TPCN  ++ L D     I+A+     
Sbjct: 18  VERTASRTMLRAVRFTEEDFSKPVIAVAVPYTNGTPCNDHIRDLGDLVQHEIEAAGGKAI 77

Query: 74  VFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVIGGCDKNMPGGMIA 133
           +FGTP +SDG+SMGTE MKYSL+SREVIAD IE   +G  +DGV+ + GCDK +P  ++ 
Sbjct: 78  IFGTPVVSDGISMGTEAMKYSLVSREVIADAIELMTEGYQVDGVMTLSGCDKTIPAALMP 137

Query: 134 LARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQEDFEGVEKNACPSTG 193
           +AR ++ G+ +YGG+I PG    ++L IVS+FE +G  +AG++  E+   +E  ACP  G
Sbjct: 138 IARNDLVGLTLYGGSILPGQHGKQELNIVSAFEGIGAHSAGKIDAEELHEIECRACPGAG 197

Query: 194 SCGGMYTANTMSSSFEALGMSLLYSSTMANPDQ------EKVDSAAESARVLVEAIKQDI 247
           SCGGMYTANTM+S+ EALGMS+  S++    D+      +K   A +SAR L++ +++  
Sbjct: 198 SCGGMYTANTMASAIEALGMSMTGSASNMAVDRSNHISADKSQDAGDSARALIKLLQKGT 257

Query: 248 KPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRKVPVICNL 307
             R I+TRK+ ENA+ +  A GGSTNAVLH LA+A+ A V  T+ D  +I  KVP++ N 
Sbjct: 258 TARQIMTRKAFENALTVAWALGGSTNAVLHLLALANEAHVPLTLKDISKITAKVPLLGNF 317

Query: 308 KPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTPRADQDVI 367
           KP G+Y+  DLH+ GG+P VMK+LL AG LHGDCLT+TG+T+AE L + PD P ADQDV 
Sbjct: 318 KPFGRYLMNDLHELGGVPMVMKVLLDAGFLHGDCLTVTGQTIAENLVSAPDLP-ADQDVC 376

Query: 368 LPIEKALYAEG-HLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEAILADKI 426
            PI+      G H+ IL GNLA EG V K +G     ++GPARVF+ E+ A+ AIL+  I
Sbjct: 377 FPIDAPYAPAGRHIRILYGNLAPEGCVLKQSGKDLNSMSGPARVFDREEEALSAILSGHI 436

Query: 427 NAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMVVGHVAP 486
              DI+V+RY GPKGGPGM EML+P++A++G GLGESV  ITDGRFSGGT G+++GHVAP
Sbjct: 437 VPKDIIVIRYEGPKGGPGMREMLSPSAALMGAGLGESVALITDGRFSGGTHGIMIGHVAP 496

Query: 487 EAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVLAKFSKL 546
           EA  GG +ALV+EGD I I+  K  L L + ++E   R+ NW++P  RY  GVL K++KL
Sbjct: 497 EAQAGGNLALVEEGDCIEINLDKQELNLVIDEQEFVLRQKNWQEPPQRYNHGVLGKYAKL 556

Query: 547 ASTASKGAVT 556
            S+ASKGAVT
Sbjct: 557 VSSASKGAVT 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: 887
Number of extensions: 41
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: 570
Length adjustment: 36
Effective length of query: 521
Effective length of database: 534
Effective search space:   278214
Effective search space used:   278214
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_092348740.1 BLU87_RS11915 (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.28350.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     6e-207  674.4   3.6   6.9e-207  674.2   3.6    1.0  1  lcl|NCBI__GCF_900107645.1:WP_092348740.1  BLU87_RS11915 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900107645.1:WP_092348740.1  BLU87_RS11915 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  674.2   3.6  6.9e-207  6.9e-207       1     541 [.      22     566 ..      22     568 .. 0.98

  Alignments for each domain:
  == domain 1  score: 674.2 bits;  conditional E-value: 6.9e-207
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               a+r++l+a+ +++ed++kP+iav+  yt+ +P++ h++dl++lv++eieaaGg+a  f+t  vsDGi+m
  lcl|NCBI__GCF_900107645.1:WP_092348740.1  22 ASRTMLRAVRFTEEDFSKPVIAVAVPYTNGTPCNDHIRDLGDLVQHEIEAAGGKAIIFGTPVVSDGISM 90 
                                               579****************************************************************** PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               g+e mkysL+sre+iaD++e + ++ ++D+++++s CDk +P +lm  +r ++  +  +GG++ +g+  
  lcl|NCBI__GCF_900107645.1:WP_092348740.1  91 GTEAMKYSLVSREVIADAIELMTEGYQVDGVMTLSGCDKTIPAALMPIARNDLVGLTLYGGSILPGQHG 159
                                               *******************************************************************99 PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                 +++++v++fe++g+ +agk++ eel+eie  acP+agsC+G++tan+ma++ ealG+s+ gs++ +a
  lcl|NCBI__GCF_900107645.1:WP_092348740.1 160 -KQELNIVSAFEGIGAHSAGKIDAEELHEIECRACPGAGSCGGMYTANTMASAIEALGMSMTGSASNMA 227
                                               .79***************************************************************999 PP

                                 TIGR00110 208 t......saekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeag 270
                                               +      sa+k + a  s++ +++l++k  + r+i+t++afena+t+  alGGstn+vLhlla+a+ea+
  lcl|NCBI__GCF_900107645.1:WP_092348740.1 228 VdrsnhiSADKSQDAGDSARALIKLLQKGTTARQIMTRKAFENALTVAWALGGSTNAVLHLLALANEAH 296
                                               833333357899999999*************************************************** PP

                                 TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlek 339
                                               v l+l+d+ +++ kvPll+++kP g+++++dlh+ GGv++v+k+l  +g lh d+ltvtG+t+ae+l +
  lcl|NCBI__GCF_900107645.1:WP_092348740.1 297 VPLTLKDISKITAKVPLLGNFKPFGRYLMNDLHELGGVPMVMKVLLDAGFLHGDCLTVTGQTIAENLVS 365
                                               ********************************************************************* PP

                                 TIGR00110 340 vkvlrvdqdvirsldnpvkkeg.glavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeail 407
                                               ++ l++dqdv  ++d p+   g ++++L+Gnla+eG+v k++g++     + Gpa+vf+ eeeal ail
  lcl|NCBI__GCF_900107645.1:WP_092348740.1 366 APDLPADQDVCFPIDAPYAPAGrHIRILYGNLAPEGCVLKQSGKDL--NSMSGPARVFDREEEALSAIL 432
                                               ******************988769*******************865..899****************** PP

                                 TIGR00110 408 ggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaeg 476
                                               +g++   d++viryeGPkGgPGmremL P++al+g+GLg++vaLitDGrfsGgt+G++iGhv+Pea +g
  lcl|NCBI__GCF_900107645.1:WP_092348740.1 433 SGHIVPKDIIVIRYEGPKGGPGMREMLSPSAALMGAGLGESVALITDGRFSGGTHGIMIGHVAPEAQAG 501
                                               ********************************************************************* PP

                                 TIGR00110 477 GaialvedGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541
                                               G++alve+GD i+i++++++l+l ++e+e+  r+++++++ +r+ +g+L kyaklvssa+kGav+
  lcl|NCBI__GCF_900107645.1:WP_092348740.1 502 GNLALVEEGDCIEINLDKQELNLVIDEQEFVLRQKNWQEPPQRYNHGVLGKYAKLVSSASKGAVT 566
                                               ***************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (570 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: 11.80
//
[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