Alignments for a candidate for ilvD in Desulfitobacterium hafniense DCB-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Desulfitobacterium hafniense DCB-2

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_015944057.1 DHAF_RS12305 dihydroxy-acid dehydratase

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



>NCBI__GCF_000021925.1:WP_015944057.1
          Length = 563

 Score =  567 bits (1461), Expect = e-166
 Identities = 308/560 (55%), Positives = 387/560 (69%), Gaps = 12/560 (2%)

Query: 1   MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60
           M S+TIK GI RAPHRSLL   GLTD +  KPFIG+ NS+T++VPGH+HLR++ EAVK G
Sbjct: 1   MNSNTIKTGIDRAPHRSLLKALGLTDRELSKPFIGVVNSFTELVPGHMHLRQVTEAVKAG 60

Query: 61  VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120
           +   GG  FEF+T+A+CDGIAM H+GM YSLASREIVAD +E MA  H LD LVL+P+CD
Sbjct: 61  IRENGGTPFEFSTIAVCDGIAMGHEGMHYSLASREIVADAIEVMAKGHQLDALVLIPSCD 120

Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180
           K+VPGMLMAA RL+IPAIVV+GGPMLPG F+G  V L  V+EGVG V AG+  E  L EL
Sbjct: 121 KVVPGMLMAAMRLNIPAIVVSGGPMLPGRFEGNPVTLSTVFEGVGQVHAGKKDEAWLHEL 180

Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240
           E  ACP   SCAG+FTAN+M CLTEALGM+LPG  T  AV S +  +A+ +G +++E+ +
Sbjct: 181 EAKACPTCGSCAGMFTANSMNCLTEALGMALPGNGTIPAVYSERLVLAKETGYQVMELYR 240

Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300
           ++LKP  I++Q   +N V VD+ALG STNT LH+PAIA E D ++ +L   +E+S   P 
Sbjct: 241 QDLKPRDIVTQSTLKNGVAVDMALGCSTNTILHLPAIANEGD-IDWDLGKVNEVSEKTPQ 299

Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTLEDH--INRECVTCTGRTVQENIENVKVGHRDV 358
           I  ++PA E  +  L  AGG+ AVLK L D   I+   +T +G T+ E +++ KV   ++
Sbjct: 300 ICKLAPASETPLAALHEAGGVSAVLKQLLDAGLIDGSTMTVSGVTMAERLKDAKVVDTEI 359

Query: 359 IRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGG 418
           IRP  +P    GGL IL GNLAP G+V+KQGA++    V EG AKVFN E    EAI   
Sbjct: 360 IRPQSNPFSQRGGLRILFGNLAPEGAVIKQGALSSQDFVFEGSAKVFNGEVPAAEAIRNL 419

Query: 419 RIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGLER-VALITDGRFSGGTRGPCVGHV 477
            I  GDV+VIRYEGPKGGPGMREML PT+ +AGMGL+  VAL+TDGRFSG +RG  +GHV
Sbjct: 420 EIKAGDVVVIRYEGPKGGPGMREMLGPTATLAGMGLDSDVALLTDGRFSGASRGLSIGHV 479

Query: 478 SPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQS----AVKPRRSV----K 529
           SPEA   G +A + DGD IRIDI   +LE  +S  E E+R Q     AVKP        +
Sbjct: 480 SPEAALGGDIALLKDGDKIRIDIGKGRLEWIVSEEEREQRRQEFAAMAVKPDHLKPELRQ 539

Query: 530 GWLARYRKLAGSADTGAVLR 549
           G+L RY     SA  GA LR
Sbjct: 540 GYLGRYAYFVQSASKGAALR 559


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: 944
Number of extensions: 43
Number of successful extensions: 5
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: 563
Length adjustment: 36
Effective length of query: 513
Effective length of database: 527
Effective search space:   270351
Effective search space used:   270351
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 WP_015944057.1 DHAF_RS12305 (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.30562.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.3e-235  767.6   0.6   3.8e-235  767.4   0.6    1.0  1  lcl|NCBI__GCF_000021925.1:WP_015944057.1  DHAF_RS12305 dihydroxy-acid dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021925.1:WP_015944057.1  DHAF_RS12305 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  767.4   0.6  3.8e-235  3.8e-235       1     542 [.      14     559 ..      14     560 .. 0.99

  Alignments for each domain:
  == domain 1  score: 767.4 bits;  conditional E-value: 3.8e-235
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++r+llka+Gl+d +l+kP+i+vvns+te+vPgh+hl++++++vk++i+++Gg+++ef tiav+DGiam
  lcl|NCBI__GCF_000021925.1:WP_015944057.1  14 PHRSLLKALGLTDRELSKPFIGVVNSFTELVPGHMHLRQVTEAVKAGIRENGGTPFEFSTIAVCDGIAM 82 
                                               69******************************************************************* PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               gheGm+ysL+srei+aD++e ++k+h+lDalv+i+sCDk+vPGmlmaa+rlniPaivvsGGpm +g+++
  lcl|NCBI__GCF_000021925.1:WP_015944057.1  83 GHEGMHYSLASREIVADAIEVMAKGHQLDALVLIPSCDKVVPGMLMAAMRLNIPAIVVSGGPMLPGRFE 151
                                               ********************************************************************* PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                ++ ++l+ vfe+vg+++agk +e+ l+e+e  acPt+gsC+G+ftansm+cltealG++lPg++t++a
  lcl|NCBI__GCF_000021925.1:WP_015944057.1 152 -GNPVTLSTVFEGVGQVHAGKKDEAWLHELEAKACPTCGSCAGMFTANSMNCLTEALGMALPGNGTIPA 219
                                               .9******************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                               + +e++ lak++g +++el ++++kPrdi+t+++++n +++d+alG stnt+Lhl+aia+e +++ +l 
  lcl|NCBI__GCF_000021925.1:WP_015944057.1 220 VYSERLVLAKETGYQVMELYRQDLKPRDIVTQSTLKNGVAVDMALGCSTNTILHLPAIANEGDIDWDLG 288
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345
                                               +++++s+k+P+++kl+P++++ ++ lh+aGGvsavlk+l  +gl++  ++tv+G t+ae+l+++kv   
  lcl|NCBI__GCF_000021925.1:WP_015944057.1 289 KVNEVSEKTPQICKLAPASETPLAALHEAGGVSAVLKQLLDAGLIDGSTMTVSGVTMAERLKDAKVV-- 355
                                               ******************************************************************9.. PP

                                 TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                               d+++ir+ +np+++ ggl++L+Gnla+eGav+k+++ +++  +feG+akvf+ e  a eai + ++k+G
  lcl|NCBI__GCF_000021925.1:WP_015944057.1 356 DTEIIRPQSNPFSQRGGLRILFGNLAPEGAVIKQGALSSQDFVFEGSAKVFNGEVPAAEAIRNLEIKAG 424
                                               ********************************************************************* PP

                                 TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483
                                               dvvviryeGPkGgPGmremL Pt++l+g+GL+++vaL+tDGrfsG++rGlsiGhvsPeaa gG ial++
  lcl|NCBI__GCF_000021925.1:WP_015944057.1 425 DVVVIRYEGPKGGPGMREMLGPTATLAGMGLDSDVALLTDGRFSGASRGLSIGHVSPEAALGGDIALLK 493
                                               ********************************************************************* PP

                                 TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkea.......revkgaLakyaklvssadkGavld 542
                                               dGDki+iDi + +l+  vseee ++rr++  +          +  +g+L +ya +v+sa+kGa+l+
  lcl|NCBI__GCF_000021925.1:WP_015944057.1 494 DGDKIRIDIGKGRLEWIVSEEEREQRRQEFAAMAVkpdhlkpELRQGYLGRYAYFVQSASKGAALR 559
                                               ****************************988776666778877789*****************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (563 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: 8.29
//
[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