Alignments for a candidate for ilvD in Methylobacterium sp. 4-46

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Methylobacterium sp. 4-46

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_012334770.1 M446_RS24325 dihydroxy-acid dehydratase

Query= SwissProt::P9WKJ5
         (575 letters)



>NCBI__GCF_000019365.1:WP_012334770.1
          Length = 577

 Score =  550 bits (1418), Expect = e-161
 Identities = 295/555 (53%), Positives = 370/555 (66%), Gaps = 8/555 (1%)

Query: 21  SRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLANAVKEGVF 80
           SR VT+G  +A  R  L A+G+  E   +P +GVAS WNE  PCN++L R A AVK+GV 
Sbjct: 14  SRHVTEGPARAPHRSYLYAMGLTREQIHQPLVGVASCWNEAAPCNIALMRQAQAVKKGVA 73

Query: 81  SAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLAGCDKS 140
           +A G P EF TI+V+DGI+MGH GM  SL SREVIADSVE+ M+    D  V LAGCDKS
Sbjct: 74  AAAGTPREFCTITVTDGIAMGHRGMRASLPSREVIADSVELTMRGHAYDALVGLAGCDKS 133

Query: 141 LPGMLMAAARLDLAAVFLYAGSILPGRAKLSDGSERDVTIIDAFEAVGACSRGLMSRADV 200
           LPGM+MA  RL++ ++F+Y GSILPG  +      R VT+ D FEAVG  S G MS  D+
Sbjct: 134 LPGMMMAMVRLNVPSIFIYGGSILPGTFR-----GRPVTVQDLFEAVGKHSVGAMSDEDL 188

Query: 201 DAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARRSGQAVVE 260
           D +E+  CP  GACG  +TANTMA+ +EA+G++LP SA  PA    RD F   +G+ V++
Sbjct: 189 DELEQVACPSAGACGAQFTANTMATVSEAIGLALPYSAGAPAPYEIRDKFCAAAGEMVMD 248

Query: 261 LLRRGITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALSLQDFSRIGSGV 320
           LL R I  RDI+T+ A ENA  VV A GGSTNA LHL AIAHEA ++  L D + I    
Sbjct: 249 LLARNIRPRDIVTRRALENAATVVAASGGSTNAALHLPAIAHEAGISFDLFDVAEIFKRT 308

Query: 321 PHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAENLAAITPPDP 380
           P++AD+KP GR+V  D+  +GG+P++MK LLD G LHGDC+TVTG T+AENLA +   D 
Sbjct: 309 PYVADLKPGGRYVAKDLFEVGGIPLLMKTLLDHGFLHGDCMTVTGRTIAENLAKVAWNDQ 368

Query: 381 DGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGF--DSDVFEGTARVFDGERAALDA 438
              V+R    PI P+GG+  L G+LAPEGA+VK AG   D  VF G ARVFD E A  +A
Sbjct: 369 Q-DVVRPANTPITPTGGVVGLKGNLAPEGAIVKVAGMAPDRQVFAGPARVFDTEEACFEA 427

Query: 439 LEDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFSGGTTGLC 498
           +++     GD +VIRYEGPKGGPGMREMLA T A+ G G+G  V L+TDGRFSG T G C
Sbjct: 428 VQNRQYKEGDVLVIRYEGPKGGPGMREMLATTAALYGQGMGDKVALITDGRFSGATRGFC 487

Query: 499 VGHIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQDFSPPPPRYTTGVL 558
           VGH+ PEA  GGPI LL++GD IRLD     L V     E A R++ ++P     T+G L
Sbjct: 488 VGHVGPEAAVGGPIGLLKDGDIIRLDAIQGTLTVDLSDEELAERRKAWAPRGNEATSGYL 547

Query: 559 SKYVKLVSSAAVGAV 573
            KY + V  A  GAV
Sbjct: 548 WKYAQTVGPAVNGAV 562


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: 970
Number of extensions: 47
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: 575
Length of database: 577
Length adjustment: 36
Effective length of query: 539
Effective length of database: 541
Effective search space:   291599
Effective search space used:   291599
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_012334770.1 M446_RS24325 (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.20894.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-211  689.4   0.3   1.9e-211  689.2   0.3    1.0  1  lcl|NCBI__GCF_000019365.1:WP_012334770.1  M446_RS24325 dihydroxy-acid dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019365.1:WP_012334770.1  M446_RS24325 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  689.2   0.3  1.9e-211  1.9e-211       1     541 [.      25     563 ..      25     565 .. 0.99

  Alignments for each domain:
  == domain 1  score: 689.2 bits;  conditional E-value: 1.9e-211
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++r+ l+a+Gl+ e++++P+++v+++++e +P+++ l   a++vk+++ aa g++ ef ti+v+DGiam
  lcl|NCBI__GCF_000019365.1:WP_012334770.1  25 PHRSYLYAMGLTREQIHQPLVGVASCWNEAAPCNIALMRQAQAVKKGVAAAAGTPREFCTITVTDGIAM 93 
                                               699****************************************************************** PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               gh+Gm+ sLpsre+iaDsve  +++ha+Dalv ++ CDk +PGm+ma++rln+P+i+++GG++ +g ++
  lcl|NCBI__GCF_000019365.1:WP_012334770.1  94 GHRGMRASLPSREVIADSVELTMRGHAYDALVGLAGCDKSLPGMMMAMVRLNVPSIFIYGGSILPGTFR 162
                                               ********************************************************************* PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                ++ +++ d+feavg+ + g +s+e+l+e+e++acP+ag+C+  ftan+ma+++ea+Gl+lP+s+ ++a
  lcl|NCBI__GCF_000019365.1:WP_012334770.1 163 -GRPVTVQDLFEAVGKHSVGAMSDEDLDELEQVACPSAGACGAQFTANTMATVSEAIGLALPYSAGAPA 230
                                               .9******************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                                 + + +++  +g+ +++l+ +ni+Prdi+t++a+ena t++ a GGstn+ Lhl+aia+eag++++l 
  lcl|NCBI__GCF_000019365.1:WP_012334770.1 231 PYEIRDKFCAAAGEMVMDLLARNIRPRDIVTRRALENAATVVAASGGSTNAALHLPAIAHEAGISFDLF 299
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345
                                               d+ ++ +++P +a+lkP+g++v +dl ++GG++ ++k+l  +g lh d++tvtG+t+ae+l+kv  +  
  lcl|NCBI__GCF_000019365.1:WP_012334770.1 300 DVAEIFKRTPYVADLKPGGRYVAKDLFEVGGIPLLMKTLLDHGFLHGDCMTVTGRTIAENLAKVAWN-D 367
                                               ****************************************************************999.8 PP

                                 TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                               +qdv+r+ + p++ +gg+  LkGnla+eGa+vk+ag++ d  +f Gpa+vf+ ee++ ea+ +++ keG
  lcl|NCBI__GCF_000019365.1:WP_012334770.1 368 QQDVVRPANTPITPTGGVVGLKGNLAPEGAIVKVAGMAPDRQVFAGPARVFDTEEACFEAVQNRQYKEG 436
                                               99******************************************************************* PP

                                 TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483
                                               dv+viryeGPkGgPGmremLa t+al g G+g+kvaLitDGrfsG+trG+++Ghv Peaa+gG+i+l++
  lcl|NCBI__GCF_000019365.1:WP_012334770.1 437 DVLVIRYEGPKGGPGMREMLATTAALYGQGMGDKVALITDGRFSGATRGFCVGHVGPEAAVGGPIGLLK 505
                                               ********************************************************************* PP

                                 TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541
                                               dGD+i++D+ + +l +++s+eelaerr+++ +++++ ++g+L kya+ v  a +Gav+
  lcl|NCBI__GCF_000019365.1:WP_012334770.1 506 DGDIIRLDAIQGTLTVDLSDEELAERRKAWAPRGNEATSGYLWKYAQTVGPAVNGAVT 563
                                               ********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (577 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: 11.99
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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