Alignments for a candidate for ilvD in Bradyrhizobium sp. BTAi1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Bradyrhizobium sp. BTAi1

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_012044488.1 BBTA_RS20815 dihydroxy-acid dehydratase

Query= SwissProt::P9WKJ5
         (575 letters)



>NCBI__GCF_000015165.1:WP_012044488.1
          Length = 574

 Score =  546 bits (1407), Expect = e-160
 Identities = 291/560 (51%), Positives = 372/560 (66%), Gaps = 8/560 (1%)

Query: 16  DIKPR--SRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLAN 73
           DIK R  SR VT+G E+A  R  L A+G+      +P +GVAS WNE  PCN++L R A 
Sbjct: 6   DIKRRLPSRHVTEGPERAPHRSYLYAMGLTTAQIHQPFVGVASCWNEAAPCNIALMRQAQ 65

Query: 74  AVKEGVFSAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVL 133
           AVK+GV  AGG P EF TI+V+DGI+MGH+GM  SL SRE IADSVE+ ++    D  V 
Sbjct: 66  AVKKGVAHAGGTPREFCTITVTDGIAMGHDGMRSSLPSRETIADSVELTIRGHAYDALVG 125

Query: 134 LAGCDKSLPGMLMAAARLDLAAVFLYAGSILPGRAKLSDGSERDVTIIDAFEAVGACSRG 193
           LAGCDKSLPGM+MA  RL++ ++F+Y GSILPG  +      + VT+ D FEAVG  S G
Sbjct: 126 LAGCDKSLPGMMMAMVRLNVPSIFIYGGSILPGNFR-----GQQVTVQDMFEAVGKHSVG 180

Query: 194 LMSRADVDAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARR 253
            MS  D+D +ER  CP  GACG  +TANTMA+ +EA+G++LP SA  PA    RD F   
Sbjct: 181 QMSDDDLDELERVACPSAGACGAQFTANTMATVSEAIGLALPYSAGAPAPYEIRDSFCMT 240

Query: 254 SGQAVVELLRRGITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALSLQDF 313
           +G+ V+EL+   I  RDI+T+ A ENA AVV A GGSTNA LHL AIAHEA +   L D 
Sbjct: 241 AGEKVMELIAANIRPRDIVTRAALENAAAVVAASGGSTNAALHLPAIAHEAGIKFDLFDV 300

Query: 314 SRIGSGVPHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAENLA 373
           + I    P++AD+KP GR+V  D+   GG+P++MK LLD G L+GDCLTVTG T+AENL 
Sbjct: 301 AEIFKKTPYIADLKPGGRYVAKDMFEAGGIPLLMKTLLDHGYLNGDCLTVTGRTIAENLK 360

Query: 374 AITPPDPDGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSDVFEGTARVFDGER 433
            +   +P   V+R+   PI  +GG+  L G+LAPEGA+VK AG  +  F G AR FD E 
Sbjct: 361 GV-KWNPHQDVVRSADQPITATGGVVGLKGNLAPEGAIVKVAGMSNLKFSGPARCFDREE 419

Query: 434 AALDALEDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFSGG 493
            A +A++  T   GD +VIRYEGP+GGPGMREML  T A+ G G+G  + L+TDGRFSG 
Sbjct: 420 DAFEAVQKRTYREGDVIVIRYEGPRGGPGMREMLQTTAALTGQGMGGKIALITDGRFSGA 479

Query: 494 TTGLCVGHIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQDFSPPPPRY 553
           T G C+GHI PEA  GGPIAL+ +GD I +D     LDV    AE A+R+  ++P   ++
Sbjct: 480 TRGFCIGHIGPEAAIGGPIALVEDGDIIEIDAVAGRLDVKLSDAELAARKTKWTPRETQH 539

Query: 554 TTGVLSKYVKLVSSAAVGAV 573
           T+G L KY + V  A  GAV
Sbjct: 540 TSGALWKYAQQVGPAVAGAV 559


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: 51
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: 574
Length adjustment: 36
Effective length of query: 539
Effective length of database: 538
Effective search space:   289982
Effective search space used:   289982
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_012044488.1 BBTA_RS20815 (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.2095.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-212  692.8   2.0   1.8e-212  692.6   2.0    1.0  1  lcl|NCBI__GCF_000015165.1:WP_012044488.1  BBTA_RS20815 dihydroxy-acid dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015165.1:WP_012044488.1  BBTA_RS20815 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  692.6   2.0  1.8e-212  1.8e-212       1     541 [.      24     560 ..      24     562 .. 0.99

  Alignments for each domain:
  == domain 1  score: 692.6 bits;  conditional E-value: 1.8e-212
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++r+ l+a+Gl+ +++++P+++v+++++e +P+++ l   a++vk+++ +aGg++ ef ti+v+DGiam
  lcl|NCBI__GCF_000015165.1:WP_012044488.1  24 PHRSYLYAMGLTTAQIHQPFVGVASCWNEAAPCNIALMRQAQAVKKGVAHAGGTPREFCTITVTDGIAM 92 
                                               699****************************************************************** PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               gh+Gm+ sLpsre iaDsve  +++ha+Dalv ++ CDk +PGm+ma++rln+P+i+++GG++ +g+++
  lcl|NCBI__GCF_000015165.1:WP_012044488.1  93 GHDGMRSSLPSRETIADSVELTIRGHAYDALVGLAGCDKSLPGMMMAMVRLNVPSIFIYGGSILPGNFR 161
                                               ********************************************************************* PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                ++++++ d+feavg+ + g++s+++l+e+er+acP+ag+C+  ftan+ma+++ea+Gl+lP+s+ ++a
  lcl|NCBI__GCF_000015165.1:WP_012044488.1 162 -GQQVTVQDMFEAVGKHSVGQMSDDDLDELERVACPSAGACGAQFTANTMATVSEAIGLALPYSAGAPA 229
                                               .9******************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                                 + + +++ ++g++++el+  ni+Prdi+t++a+ena +++ a GGstn+ Lhl+aia+eag+k++l 
  lcl|NCBI__GCF_000015165.1:WP_012044488.1 230 PYEIRDSFCMTAGEKVMELIAANIRPRDIVTRAALENAAAVVAASGGSTNAALHLPAIAHEAGIKFDLF 298
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345
                                               d+ ++ +k+P +a+lkP+g++v +d+ +aGG++ ++k+l  +g+l+ d+ltvtG+t+ae+l+ vk +  
  lcl|NCBI__GCF_000015165.1:WP_012044488.1 299 DVAEIFKKTPYIADLKPGGRYVAKDMFEAGGIPLLMKTLLDHGYLNGDCLTVTGRTIAENLKGVKWN-P 366
                                               ******************************************************************9.8 PP

                                 TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                               +qdv+rs d+p++++gg+  LkGnla+eGa+vk+ag+++  lkf Gpa+ f+ ee+a ea+ ++  +eG
  lcl|NCBI__GCF_000015165.1:WP_012044488.1 367 HQDVVRSADQPITATGGVVGLKGNLAPEGAIVKVAGMSN--LKFSGPARCFDREEDAFEAVQKRTYREG 433
                                               9**************************************..**************************** PP

                                 TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483
                                               dv+viryeGP+GgPGmremL+ t+al+g G+g k+aLitDGrfsG+trG++iGh+ Peaa gG+ialve
  lcl|NCBI__GCF_000015165.1:WP_012044488.1 434 DVIVIRYEGPRGGPGMREMLQTTAALTGQGMGGKIALITDGRFSGATRGFCIGHIGPEAAIGGPIALVE 502
                                               ********************************************************************* PP

                                 TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541
                                               dGD+i+iD+ + +ld+++s++ela+r+ k++++e+++++gaL kya+ v  a  Gav+
  lcl|NCBI__GCF_000015165.1:WP_012044488.1 503 DGDIIEIDAVAGRLDVKLSDAELAARKTKWTPRETQHTSGALWKYAQQVGPAVAGAVT 560
                                               ********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (574 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: 8.81
//
[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