Alignments for a candidate for ilvD in Mycolicibacterium vanbaalenii PYR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Mycolicibacterium vanbaalenii PYR-1

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_011777498.1 MVAN_RS00890 dihydroxy-acid dehydratase

Query= SwissProt::P9WKJ5
         (575 letters)



>NCBI__GCF_000015305.1:WP_011777498.1
          Length = 565

 Score =  979 bits (2532), Expect = 0.0
 Identities = 495/559 (88%), Positives = 523/559 (93%)

Query: 16  DIKPRSRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLANAV 75
           DIKPRSRDVTDGLEKAAARGMLRAVGM DEDFAKPQIGV SSWNEITPCNLSLDRLA AV
Sbjct: 6   DIKPRSRDVTDGLEKAAARGMLRAVGMGDEDFAKPQIGVGSSWNEITPCNLSLDRLAKAV 65

Query: 76  KEGVFSAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLA 135
           KEGVF AGG+P+EFGTISVSDGISMGHEGMHFSLVSRE+IADSVE VMQAERLDGSVLLA
Sbjct: 66  KEGVFEAGGFPMEFGTISVSDGISMGHEGMHFSLVSREIIADSVETVMQAERLDGSVLLA 125

Query: 136 GCDKSLPGMLMAAARLDLAAVFLYAGSILPGRAKLSDGSERDVTIIDAFEAVGACSRGLM 195
           GCDKSLPGMLMAAARLDLA+VFLYAGSILPGR KLSDGSE+DVTIIDAFEAVGAC+RGLM
Sbjct: 126 GCDKSLPGMLMAAARLDLASVFLYAGSILPGRVKLSDGSEKDVTIIDAFEAVGACARGLM 185

Query: 196 SRADVDAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARRSG 255
            R DVDAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFAR+SG
Sbjct: 186 PREDVDAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARKSG 245

Query: 256 QAVVELLRRGITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALSLQDFSR 315
            AVVELLRRGITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIA+EANV L+L+DF+R
Sbjct: 246 MAVVELLRRGITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAYEANVKLTLEDFTR 305

Query: 316 IGSGVPHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAENLAAI 375
           +G+ VPHLADVKPFG +VM+DVD IGGVPVVMKALLDAGLLHGDCLTVTG TMAENLA I
Sbjct: 306 VGAKVPHLADVKPFGAYVMNDVDRIGGVPVVMKALLDAGLLHGDCLTVTGKTMAENLAHI 365

Query: 376 TPPDPDGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSDVFEGTARVFDGERAA 435
            PPDPDGKVLRAL+ PIHP+GGITILHGSLAPEGAVVK+AGFDSDVFEGTARVF+ ERAA
Sbjct: 366 APPDPDGKVLRALSRPIHPTGGITILHGSLAPEGAVVKSAGFDSDVFEGTARVFERERAA 425

Query: 436 LDALEDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFSGGTT 495
           LDALEDGTIT GD VVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLL+TDGRFSGGTT
Sbjct: 426 LDALEDGTITHGDVVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLMTDGRFSGGTT 485

Query: 496 GLCVGHIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQDFSPPPPRYTT 555
           GLCVGHIAPEAVDGGPIA +++GD+IRLDVA   LDV+ D  EF +R+  F P PP YTT
Sbjct: 486 GLCVGHIAPEAVDGGPIAFIKDGDKIRLDVAKGTLDVVVDKDEFEARKVGFEPLPPVYTT 545

Query: 556 GVLSKYVKLVSSAAVGAVC 574
           GVL+KY KLV SAA GAVC
Sbjct: 546 GVLAKYTKLVGSAATGAVC 564


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: 1345
Number of extensions: 46
Number of successful extensions: 2
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: 565
Length adjustment: 36
Effective length of query: 539
Effective length of database: 529
Effective search space:   285131
Effective search space used:   285131
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_011777498.1 MVAN_RS00890 (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.25718.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.7e-220  716.7   5.0   9.9e-220  716.6   5.0    1.0  1  lcl|NCBI__GCF_000015305.1:WP_011777498.1  MVAN_RS00890 dihydroxy-acid dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_011777498.1  MVAN_RS00890 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  716.6   5.0  9.9e-220  9.9e-220       2     541 ..      23     564 ..      22     565 .] 0.99

  Alignments for each domain:
  == domain 1  score: 716.6 bits;  conditional E-value: 9.9e-220
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               ar +l+a+G+ ded+ kP+i+v++s++ei+P++++l+ lak+vke++ +aGg ++ef+ti+vsDGi+mg
  lcl|NCBI__GCF_000015305.1:WP_011777498.1  23 ARGMLRAVGMGDEDFAKPQIGVGSSWNEITPCNLSLDRLAKAVKEGVFEAGGFPMEFGTISVSDGISMG 91 
                                               799****************************************************************** PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               heGm++sL+sreiiaDsvetv++a++lD+ v+++ CDk +PGmlmaa+rl++ +++ + G++ +g++kl
  lcl|NCBI__GCF_000015305.1:WP_011777498.1  92 HEGMHFSLVSREIIADSVETVMQAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFLYAGSILPGRVKL 160
                                               ********************************************************************9 PP

                                 TIGR00110 140 ....sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsst 204
                                                    ++++++d+feavg++a g +  e++++ier  cP+ g+C+G++tan+ma+++ealG+slPgs++
  lcl|NCBI__GCF_000015305.1:WP_011777498.1 161 sdgsEKDVTIIDAFEAVGACARGLMPREDVDAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAA 229
                                               6665579************************************************************** PP

                                 TIGR00110 205 llatsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvkl 273
                                                +at+ ++  +a+ksg+ +vel+++ i+ rdiltkeafenai++++a GGstn+vLhllaia ea+vkl
  lcl|NCBI__GCF_000015305.1:WP_011777498.1 230 PPATDRRRDGFARKSGMAVVELLRRGITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAYEANVKL 298
                                               ********************************************************************* PP

                                 TIGR00110 274 slddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkv 342
                                               +l+df r+  kvP+la++kP g +v++d++r GGv+ v+k l  +gllh d+ltvtGkt+ae+l+++  
  lcl|NCBI__GCF_000015305.1:WP_011777498.1 299 TLEDFTRVGAKVPHLADVKPFGAYVMNDVDRIGGVPVVMKALLDAGLLHGDCLTVTGKTMAENLAHIAP 367
                                               *******************************************************************99 PP

                                 TIGR00110 343 lrvdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkv 411
                                                  d +v+r+l+ p++ +gg+ +L+G+la+eGavvk ag ++   +feG+a+vfe e +al+a+ +g +
  lcl|NCBI__GCF_000015305.1:WP_011777498.1 368 PDPDGKVLRALSRPIHPTGGITILHGSLAPEGAVVKSAGFDS--DVFEGTARVFERERAALDALEDGTI 434
                                               988999************************************..679********************** PP

                                 TIGR00110 412 keGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaia 480
                                               ++GdvvviryeGPkGgPGmremLa t a++g+GLgk+v L+tDGrfsGgt+Gl++Gh++Pea+ gG+ia
  lcl|NCBI__GCF_000015305.1:WP_011777498.1 435 THGDVVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLMTDGRFSGGTTGLCVGHIAPEAVDGGPIA 503
                                               ********************************************************************* PP

                                 TIGR00110 481 lvedGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541
                                               +++dGDki++D+ + +ld+ v+++e+++r+   ++  + ++ g+Laky+klv sa +Gav 
  lcl|NCBI__GCF_000015305.1:WP_011777498.1 504 FIKDGDKIRLDVAKGTLDVVVDKDEFEARKVGFEPLPPVYTTGVLAKYTKLVGSAATGAVC 564
                                               ***********************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (565 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: 9.93
//
[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