Alignments for a candidate for ilvD in Acidimicrobium ferrooxidans DSM 10331

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Acidimicrobium ferrooxidans DSM 10331

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_015798949.1 AFER_RS08025 dihydroxy-acid dehydratase

Query= SwissProt::P9WKJ5
         (575 letters)



>NCBI__GCF_000023265.1:WP_015798949.1
          Length = 567

 Score =  704 bits (1817), Expect = 0.0
 Identities = 362/557 (64%), Positives = 426/557 (76%), Gaps = 5/557 (0%)

Query: 17  IKPRSRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLANAVK 76
           +K RSRDVT+G  +A AR MLRAVG+ +EDF KPQI VASSWNE+TPCNL L  LA  VK
Sbjct: 6   LKVRSRDVTEGPTRAPARAMLRAVGLVEEDFDKPQIAVASSWNEVTPCNLPLGELAKRVK 65

Query: 77  EGVFSAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLAG 136
            GV SAGG PLEF TI+VSDGISMGHEGMH SLVSREVIADSVE+++ AER+DG V LAG
Sbjct: 66  AGVRSAGGVPLEFATIAVSDGISMGHEGMHSSLVSREVIADSVELMVHAERMDGLVTLAG 125

Query: 137 CDKSLPGMLMAAARLDLAAVFLYAGSILPGRAKLSDGSERDVTIIDAFEAVGACSRGLMS 196
           CDKSLPGM+MAAARLDLA+VF+Y GSILPG  K     ++ + I+  FEAVGA + G +S
Sbjct: 126 CDKSLPGMMMAAARLDLASVFVYGGSILPGHLK-----DQRLDIVSVFEAVGAYAAGQIS 180

Query: 197 RADVDAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARRSGQ 256
           + ++ AIER  CP  G+C GMYTANTMAS +EALG++  GSA+ PA DRRR   A  +G+
Sbjct: 181 QDELSAIERNACPTPGSCAGMYTANTMASVSEALGLAPLGSASAPAVDRRRADAAFEAGE 240

Query: 257 AVVELLRRGITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALSLQDFSRI 316
            V+  L  GITAR ILTKEAFENAIA VMA GGSTNAVLHL+AIA+EA V L L DF+RI
Sbjct: 241 LVMRQLELGITARRILTKEAFENAIATVMALGGSTNAVLHLMAIANEARVELRLDDFNRI 300

Query: 317 GSGVPHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAENLAAIT 376
            + VPHLAD KP G+  M+D+D +GGVPVV++ L +AGL+H D LT TG T+ + L A  
Sbjct: 301 AARVPHLADTKPHGKFYMTDIDRVGGVPVVLRELAEAGLVHTDVLTATGRTLGDELDAYD 360

Query: 377 PPDPDGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSDVFEGTARVFDGERAAL 436
           PP  DG V+  L +PIH  GGI +L GSLAP G+VVK AG D DVFEGTARVFD E AAL
Sbjct: 361 PPAADGVVIHRLDDPIHAVGGIAVLTGSLAPRGSVVKVAGIDQDVFEGTARVFDREEAAL 420

Query: 437 DALEDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFSGGTTG 496
            A+  G I  GD VVIRYEGPKGGPGMREMLA+TGA+KGAG G D  L+TDGRFSGGT G
Sbjct: 421 TAILAGEIRAGDVVVIRYEGPKGGPGMREMLAVTGAMKGAGRGSDAALVTDGRFSGGTHG 480

Query: 497 LCVGHIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQDFSPPPPRYTTG 556
           LCVGH+APEA DGGPIAL+R+GDRIR+DV    +D+L  P E   R+  F+P PPRYT+G
Sbjct: 481 LCVGHVAPEAADGGPIALVRDGDRIRIDVPNHAIDLLVAPDELERRRASFAPLPPRYTSG 540

Query: 557 VLSKYVKLVSSAAVGAV 573
            L+K+  LV  A VGAV
Sbjct: 541 ALAKFAALVRGADVGAV 557


Lambda     K      H
   0.318    0.136    0.393 

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: 1035
Number of extensions: 44
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: 575
Length of database: 567
Length adjustment: 36
Effective length of query: 539
Effective length of database: 531
Effective search space:   286209
Effective search space used:   286209
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_015798949.1 AFER_RS08025 (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.18318.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.6e-228  743.8   3.9   6.4e-228  743.6   3.9    1.0  1  lcl|NCBI__GCF_000023265.1:WP_015798949.1  AFER_RS08025 dihydroxy-acid dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000023265.1:WP_015798949.1  AFER_RS08025 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  743.6   3.9  6.4e-228  6.4e-228       1     542 [.      21     559 ..      21     560 .. 0.99

  Alignments for each domain:
  == domain 1  score: 743.6 bits;  conditional E-value: 6.4e-228
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               +ara+l+a+Gl +ed++kP+iav++s++e++P+++ l +lak+vk+++++aGgv+ ef tiavsDGi+m
  lcl|NCBI__GCF_000023265.1:WP_015798949.1  21 PARAMLRAVGLVEEDFDKPQIAVASSWNEVTPCNLPLGELAKRVKAGVRSAGGVPLEFATIAVSDGISM 89 
                                               579****************************************************************** PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               gheGm+ sL+sre+iaDsve +v+a+++D+lv+++ CDk +PGm+maa+rl++ +++v+GG++ +g++k
  lcl|NCBI__GCF_000023265.1:WP_015798949.1  90 GHEGMHSSLVSREVIADSVELMVHAERMDGLVTLAGCDKSLPGMMMAAARLDLASVFVYGGSILPGHLK 158
                                               ********************************************************************* PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                 +++d+v+vfeavg+yaag++s++el++ier+acPt+gsC+G++tan+ma+++ealGl+  gs++++a
  lcl|NCBI__GCF_000023265.1:WP_015798949.1 159 -DQRLDIVSVFEAVGAYAAGQISQDELSAIERNACPTPGSCAGMYTANTMASVSEALGLAPLGSASAPA 226
                                               .8******************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                               ++ ++++ a ++g+ ++  ++  i+ r+iltkeafenai+ ++alGGstn+vLhl+aia+ea v+l ld
  lcl|NCBI__GCF_000023265.1:WP_015798949.1 227 VDRRRADAAFEAGELVMRQLELGITARRILTKEAFENAIATVMALGGSTNAVLHLMAIANEARVELRLD 295
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345
                                               df+r++ +vP+la+ kP gk +++d++r+GGv+ vl+el ++gl+h+d+lt tG+tl+++l+ ++   +
  lcl|NCBI__GCF_000023265.1:WP_015798949.1 296 DFNRIAARVPHLADTKPHGKFYMTDIDRVGGVPVVLRELAEAGLVHTDVLTATGRTLGDELDAYDPPAA 364
                                               *******************************************************************99 PP

                                 TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                               d  vi+ ld+p+++ gg+avL+G+la++G+vvk+ag+++   +feG+a+vf+ ee+al ail+g++++G
  lcl|NCBI__GCF_000023265.1:WP_015798949.1 365 DGVVIHRLDDPIHAVGGIAVLTGSLAPRGSVVKVAGIDQ--DVFEGTARVFDREEAALTAILAGEIRAG 431
                                               999************************************..679************************* PP

                                 TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483
                                               dvvviryeGPkGgPGmremLa t a++g+G g++ aL+tDGrfsGgt+Gl++Ghv+Peaa gG+ialv+
  lcl|NCBI__GCF_000023265.1:WP_015798949.1 432 DVVVIRYEGPKGGPGMREMLAVTGAMKGAGRGSDAALVTDGRFSGGTHGLCVGHVAPEAADGGPIALVR 500
                                               ********************************************************************* PP

                                 TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               dGD+i+iD++n+++dl v  +el++rra+  +  +r+++gaLak+a lv++ad Gav++
  lcl|NCBI__GCF_000023265.1:WP_015798949.1 501 DGDRIRIDVPNHAIDLLVAPDELERRRASFAPLPPRYTSGALAKFAALVRGADVGAVTS 559
                                               ********************************************************985 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: 00:00:00.03
# Mc/sec: 7.84
//
[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