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_012042839.1 BBTA_RS12445 dihydroxy-acid dehydratase

Query= SwissProt::P9WKJ5
         (575 letters)



>NCBI__GCF_000015165.1:WP_012042839.1
          Length = 568

 Score =  518 bits (1335), Expect = e-151
 Identities = 265/557 (47%), Positives = 371/557 (66%), Gaps = 8/557 (1%)

Query: 18  KPRSRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLANAVKE 77
           K RSR   +GL++A  R  +RA+G+DD D AKP IG+ S   E TPCN++ D   +A K 
Sbjct: 3   KLRSRVTVEGLDRAPHRAFMRAMGLDDADIAKPMIGIVSQKGEQTPCNMTHDFQVDAAKT 62

Query: 78  GVFSAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLAGC 137
           GV  AGG P EF TISVSDGISM HEGM FSL SRE+IADS+E V+     D  +   GC
Sbjct: 63  GVSEAGGTPREFATISVSDGISMNHEGMKFSLFSRELIADSIEAVVHGLAYDALIGFGGC 122

Query: 138 DKSLPGMLMAAARLDLAAVFLYAGSILPGRAKLSDGSERDVTIIDAFEAVGACSRGLMSR 197
           DK+LPG++M   R ++ ++F+Y GS LPG+ +      + +T++D++EAVG+   G +  
Sbjct: 123 DKTLPGVMMGMVRCNVPSIFIYGGSALPGKFQ-----GKTLTVLDSYEAVGSYMTGEIDV 177

Query: 198 ADVDAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARRSGQA 257
           A ++ IER+  P  GAC G +TANTM   +EA+G+S+P  +  P     R   AR++G+ 
Sbjct: 178 ATLEGIERSCLPTIGACAGQFTANTMGMLSEAMGLSMPNVSMIPGVYAERAHVARQAGRL 237

Query: 258 VVELLRRG-ITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALSLQDFSRI 316
           ++++L RG    RDI+T++A EN  A+V A GGSTNA LHL AIA+EA +  +L D   +
Sbjct: 238 IMQMLARGGPLPRDIVTRKALENGAAIVAATGGSTNAALHLPAIANEAGIRFTLDDVGEV 297

Query: 317 GSGVPHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAENLAAIT 376
            +  P + +++P G++   DV  IGG  VV++AL+++G + G C+TVTG T+AE+  A  
Sbjct: 298 FARTPLIGNLRPGGKYTAKDVYDIGGAAVVIRALIESGHIDGSCMTVTGRTLAEDYGAAN 357

Query: 377 PPDPDGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSDVFEGTARVFDGERAAL 436
            PD  G+++   A+PI   GG+ +L G+LAP+GAV+K AG  + VFEG ARVF+ E A +
Sbjct: 358 APD--GEIVFHPASPIMAEGGVAVLKGNLAPDGAVIKVAGLKNLVFEGRARVFEDEEACV 415

Query: 437 DALEDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFSGGTTG 496
            A+       G+ ++IR EGP GGPGMREML +T  I G G+G+ V L+TDGRFSG T G
Sbjct: 416 AAVRARNYQAGEVLIIRNEGPVGGPGMREMLGVTALIYGQGMGEKVALITDGRFSGATRG 475

Query: 497 LCVGHIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQDFSPPPPRYTTG 556
           +C+G+++PEA  GGP+ALLR+GD IR+D   R LDVL D AE A+R+  +S  PPR+  G
Sbjct: 476 MCIGYVSPEAFVGGPLALLRDGDPIRIDAKARTLDVLLDDAELAARRAAWSQRPPRHRAG 535

Query: 557 VLSKYVKLVSSAAVGAV 573
            L+KY KLV  A +GAV
Sbjct: 536 ALAKYAKLVGQAPLGAV 552


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: 991
Number of extensions: 53
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: 568
Length adjustment: 36
Effective length of query: 539
Effective length of database: 532
Effective search space:   286748
Effective search space used:   286748
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_012042839.1 BBTA_RS12445 (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.11243.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-195  635.2   5.8   4.9e-195  635.0   5.8    1.0  1  lcl|NCBI__GCF_000015165.1:WP_012042839.1  BBTA_RS12445 dihydroxy-acid dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015165.1:WP_012042839.1  BBTA_RS12445 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  635.0   5.8  4.9e-195  4.9e-195       1     542 [.      17     554 ..      17     555 .. 0.99

  Alignments for each domain:
  == domain 1  score: 635.0 bits;  conditional E-value: 4.9e-195
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++ra+++a+Gl d+d+ kP+i++v+   e +P++++ +   +++k ++++aGg++ ef ti+vsDGi+m
  lcl|NCBI__GCF_000015165.1:WP_012042839.1  17 PHRAFMRAMGLDDADIAKPMIGIVSQKGEQTPCNMTHDFQVDAAKTGVSEAGGTPREFATISVSDGISM 85 
                                               69**********************************998999*************************** PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               +heGmk+sL sre+iaDs+e+vv++ a+Dal+  + CDk +PG++m+++r n+P+i+++GG+  +gk++
  lcl|NCBI__GCF_000015165.1:WP_012042839.1  86 NHEGMKFSLFSRELIADSIEAVVHGLAYDALIGFGGCDKTLPGVMMGMVRCNVPSIFIYGGSALPGKFQ 154
                                               ********************************************************************* PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                ++ ++++d +eavg+y  g+++ ++le iers+ Pt g+C+G ftan+m +l+ea+Gls+P+ s ++ 
  lcl|NCBI__GCF_000015165.1:WP_012042839.1 155 -GKTLTVLDSYEAVGSYMTGEIDVATLEGIERSCLPTIGACAGQFTANTMGMLSEAMGLSMPNVSMIPG 222
                                               .9******************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkkn.ikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsl 275
                                               + ae++++a+++g+ i++++ +    Prdi+t++a+en  +++ a+GGstn+ Lhl+aia+eag++++l
  lcl|NCBI__GCF_000015165.1:WP_012042839.1 223 VYAERAHVARQAGRLIMQMLARGgPLPRDIVTRKALENGAAIVAATGGSTNAALHLPAIANEAGIRFTL 291
                                               ******************99876257******************************************* PP

                                 TIGR00110 276 ddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr 344
                                               dd+ ++  ++Pl+++l+P+gk+  +d+ + GG   v++ l ++g+++  ++tvtG+tlae    ++   
  lcl|NCBI__GCF_000015165.1:WP_012042839.1 292 DDVGEVFARTPLIGNLRPGGKYTAKDVYDIGGAAVVIRALIESGHIDGSCMTVTGRTLAEDYGAANAP- 359
                                               **************************************************************999998. PP

                                 TIGR00110 345 vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvke 413
                                                d +++    +p+ +egg+avLkGnla++Gav+k+ag ++  l+feG+a+vfe+ee++++a+ +++ ++
  lcl|NCBI__GCF_000015165.1:WP_012042839.1 360 -DGEIVFHPASPIMAEGGVAVLKGNLAPDGAVIKVAGLKN--LVFEGRARVFEDEEACVAAVRARNYQA 425
                                               .999999999******************************..9************************** PP

                                 TIGR00110 414 GdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialv 482
                                               G+v++ir eGP GgPGmremL  t+ + g G+g+kvaLitDGrfsG+trG++iG+vsPea +gG++al+
  lcl|NCBI__GCF_000015165.1:WP_012042839.1 426 GEVLIIRNEGPVGGPGMREMLGVTALIYGQGMGEKVALITDGRFSGATRGMCIGYVSPEAFVGGPLALL 494
                                               ********************************************************************* PP

                                 TIGR00110 483 edGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               +dGD i+iD+++r+ld+ ++++ela+rra+++++ +r+  gaLakyaklv +a  Gav++
  lcl|NCBI__GCF_000015165.1:WP_012042839.1 495 RDGDPIRIDAKARTLDVLLDDAELAARRAAWSQRPPRHRAGALAKYAKLVGQAPLGAVTH 554
                                               *********************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (568 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: 10.47
//
[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