Alignments for a candidate for ilvD in Methylobacterium nodulans ORS 2060

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Methylobacterium nodulans ORS 2060

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_015931822.1 MNOD_RS25405 dihydroxy-acid dehydratase

Query= SwissProt::P9WKJ5
         (575 letters)



>NCBI__GCF_000022085.1:WP_015931822.1
          Length = 577

 Score =  556 bits (1432), Expect = e-162
 Identities = 297/563 (52%), Positives = 376/563 (66%), Gaps = 8/563 (1%)

Query: 13  TVADIKPRSRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLA 72
           T+   K  SR VT+G  +A  R  L A+G+  E   +P +GVAS WNE  PCN++L R A
Sbjct: 6   TIDKSKLPSRYVTEGPARAPHRSYLYAMGLTREQIHQPLVGVASCWNEAAPCNIALMRQA 65

Query: 73  NAVKEGVFSAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSV 132
            AVK+GV +A G P EF TI+V+DGI+MGH GM  SL SREVIADSVE+ M+    D  V
Sbjct: 66  QAVKKGVAAAAGTPREFCTITVTDGIAMGHRGMRASLPSREVIADSVELTMRGHAYDALV 125

Query: 133 LLAGCDKSLPGMLMAAARLDLAAVFLYAGSILPGRAKLSDGSERDVTIIDAFEAVGACSR 192
            LAGCDKSLPGM+MA  RL++ ++F+Y GSILPG  +      R VT+ D FEAVG  S 
Sbjct: 126 GLAGCDKSLPGMMMAMVRLNVPSIFIYGGSILPGSFR-----GRPVTVQDLFEAVGKHSV 180

Query: 193 GLMSRADVDAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFAR 252
           G MS  D+D +E+  CP  GACG  +TANTMA+ +EA+G++LP SA  PA    RD F  
Sbjct: 181 GQMSDEDLDELEQVACPSAGACGAQFTANTMATVSEAIGLALPYSAGAPAPYEIRDKFCA 240

Query: 253 RSGQAVVELLRRGITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALSLQD 312
            +G+ V++LL + I  RDI+T++A ENA  VV A GGSTNA LHL AIAHEA +   L D
Sbjct: 241 AAGEMVMDLLAKNIRPRDIITRKALENAATVVAASGGSTNAALHLPAIAHEAGIVFDLFD 300

Query: 313 FSRIGSGVPHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAENL 372
            + I    P++AD+KP GR+V  D+   GG+P++MK LLD G LHGDC+TVTG T+AENL
Sbjct: 301 VAEIFRRTPYIADLKPGGRYVAKDLFEAGGIPLLMKTLLDHGFLHGDCITVTGRTIAENL 360

Query: 373 AAITPPDPDGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSD--VFEGTARVFD 430
           A +   +PD  V+R    PI P+GG+  L G+LAPEGA+VK AG  +D  VF G ARVFD
Sbjct: 361 AKVA-WNPDQDVVRPADTPITPTGGVVGLKGNLAPEGAIVKVAGMPADRQVFAGPARVFD 419

Query: 431 GERAALDALEDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRF 490
            E A  +A+++     GD +VIRYEGPKGGPGMREMLA T A+ G G+G  V L+TDGRF
Sbjct: 420 NEEACFEAVQNRQYKEGDVLVIRYEGPKGGPGMREMLATTAALYGQGMGDKVALITDGRF 479

Query: 491 SGGTTGLCVGHIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQDFSPPP 550
           SG T G CVGH+ PEA  GGPI LL++GD IRLD    +L V     E A R++ ++P  
Sbjct: 480 SGATRGFCVGHVGPEAAIGGPIGLLKDGDIIRLDAIQGILSVDLSDEELAERRKAWTPRA 539

Query: 551 PRYTTGVLSKYVKLVSSAAVGAV 573
              T+G L KY + V  A  GAV
Sbjct: 540 NEATSGYLWKYAQTVGPAVTGAV 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: 968
Number of extensions: 45
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_015931822.1 MNOD_RS25405 (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.11189.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     3e-212  691.9   0.2   3.5e-212  691.7   0.2    1.0  1  lcl|NCBI__GCF_000022085.1:WP_015931822.1  MNOD_RS25405 dihydroxy-acid dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000022085.1:WP_015931822.1  MNOD_RS25405 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  691.7   0.2  3.5e-212  3.5e-212       1     541 [.      25     563 ..      25     565 .. 1.00

  Alignments for each domain:
  == domain 1  score: 691.7 bits;  conditional E-value: 3.5e-212
                                 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_000022085.1:WP_015931822.1  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_000022085.1:WP_015931822.1  94 GHRGMRASLPSREVIADSVELTMRGHAYDALVGLAGCDKSLPGMMMAMVRLNVPSIFIYGGSILPGSFR 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_000022085.1:WP_015931822.1 163 -GRPVTVQDLFEAVGKHSVGQMSDEDLDELEQVACPSAGACGAQFTANTMATVSEAIGLALPYSAGAPA 230
                                               .9******************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                                 + + +++  +g+ +++l+ kni+Prdi+t++a+ena t++ a GGstn+ Lhl+aia+eag+ ++l 
  lcl|NCBI__GCF_000022085.1:WP_015931822.1 231 PYEIRDKFCAAAGEMVMDLLAKNIRPRDIITRKALENAATVVAASGGSTNAALHLPAIAHEAGIVFDLF 299
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345
                                               d+ ++ r++P +a+lkP+g++v +dl +aGG++ ++k+l  +g lh d++tvtG+t+ae+l+kv  +  
  lcl|NCBI__GCF_000022085.1:WP_015931822.1 300 DVAEIFRRTPYIADLKPGGRYVAKDLFEAGGIPLLMKTLLDHGFLHGDCITVTGRTIAENLAKVAWN-P 367
                                               *****************************************************************99.8 PP

                                 TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                               dqdv+r+ d p++ +gg+  LkGnla+eGa+vk+ag+  d  +f Gpa+vf++ee++ ea+ +++ keG
  lcl|NCBI__GCF_000022085.1:WP_015931822.1 368 DQDVVRPADTPITPTGGVVGLKGNLAPEGAIVKVAGMPADRQVFAGPARVFDNEEACFEAVQNRQYKEG 436
                                               ********************************************************************* PP

                                 TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483
                                               dv+viryeGPkGgPGmremLa t+al g G+g+kvaLitDGrfsG+trG+++Ghv Peaa gG+i+l++
  lcl|NCBI__GCF_000022085.1:WP_015931822.1 437 DVLVIRYEGPKGGPGMREMLATTAALYGQGMGDKVALITDGRFSGATRGFCVGHVGPEAAIGGPIGLLK 505
                                               ********************************************************************* PP

                                 TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541
                                               dGD+i++D+ +  l +++s+eelaerr++++++ ++ ++g+L kya+ v  a +Gav+
  lcl|NCBI__GCF_000022085.1:WP_015931822.1 506 DGDIIRLDAIQGILSVDLSDEELAERRKAWTPRANEATSGYLWKYAQTVGPAVTGAVT 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: 11.28
//
[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