Alignments for a candidate for ilvD in Saccharomonospora cyanea NA-134

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Saccharomonospora cyanea NA-134

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_005454119.1 SACCYDRAFT_RS04825 dihydroxy-acid dehydratase

Query= SwissProt::P9WKJ5
         (575 letters)



>NCBI__GCF_000244975.1:WP_005454119.1
          Length = 562

 Score =  853 bits (2204), Expect = 0.0
 Identities = 432/559 (77%), Positives = 488/559 (87%), Gaps = 8/559 (1%)

Query: 16  DIKPRSRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLANAV 75
           D +PRSR+VTDGLE+ AAR MLRAVGM D DFAKPQ+GVASSWNEITPCNLSL RLA A 
Sbjct: 11  DPRPRSREVTDGLERTAARAMLRAVGMGDADFAKPQVGVASSWNEITPCNLSLRRLAEAS 70

Query: 76  KEGVFSAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLA 135
           K+GV + GGYPLEFGT+SVSDGISMGHEGMHFSLVSREVIADSVE V++AERLDG+VLLA
Sbjct: 71  KQGVHAGGGYPLEFGTLSVSDGISMGHEGMHFSLVSREVIADSVETVLEAERLDGAVLLA 130

Query: 136 GCDKSLPGMLMAAARLDLAAVFLYAGSILPGRAKLSDGSERDVTIIDAFEAVGACSRGLM 195
           GCDKSLPGMLMAAARLD+AAVF+YAGS LPGR    DG  R++TIIDAFEAVGACSRGLM
Sbjct: 131 GCDKSLPGMLMAAARLDVAAVFVYAGSTLPGRL---DG--RELTIIDAFEAVGACSRGLM 185

Query: 196 SRADVDAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARRSG 255
           SR DVD +ERA+CPGEGACGGMYTANTMA AAEALGM+LPGSA+PP+ DRRRDGFAR SG
Sbjct: 186 SREDVDRVERAVCPGEGACGGMYTANTMACAAEALGMALPGSASPPSVDRRRDGFARASG 245

Query: 256 QAVVELLRRGITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALSLQDFSR 315
           +AVV LLRRGITARD+LT+EAFENAIAVVMA GGSTNAVLHLLAIAHEA VALSL DFSR
Sbjct: 246 EAVVGLLRRGITARDVLTREAFENAIAVVMALGGSTNAVLHLLAIAHEAEVALSLDDFSR 305

Query: 316 IGSGVPHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAENLAAI 375
           +G  VPHLADVKPFGRHVM+ VD +GGVPVVMKALLDAG LHGDCLTVTG T+AENLA  
Sbjct: 306 VGDRVPHLADVKPFGRHVMTAVDRVGGVPVVMKALLDAGHLHGDCLTVTGRTVAENLAEA 365

Query: 376 TPPDPDGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSDVFEGTARVFDGERAA 435
            PP+ DG V+R L++PIHP+GG+TILHG+LAPEGAVVK+AGFD   FEG ARVFDGE+AA
Sbjct: 366 APPELDGTVIRELSDPIHPTGGVTILHGTLAPEGAVVKSAGFDRTRFEGRARVFDGEQAA 425

Query: 436 LDALEDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFSGGTT 495
           + AL +  ++ GD VVIRYEGP+GGPGMREMLA+TGAIKGAGLG+DVLLLTDGRFSGGTT
Sbjct: 426 MAALPE--LSAGDVVVIRYEGPRGGPGMREMLAVTGAIKGAGLGRDVLLLTDGRFSGGTT 483

Query: 496 GLCVGHIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQDFSPPPPRYTT 555
           GLC+GH+APEA  GGPIA +R+GD I +D++ R LD+L + AE A R+  +SPP   +  
Sbjct: 484 GLCIGHVAPEAAHGGPIAFVRDGDPIVVDLSSRTLDLLVEDAELARRRDGWSPPGIEH-R 542

Query: 556 GVLSKYVKLVSSAAVGAVC 574
           GVL KY +LV SA+ GAVC
Sbjct: 543 GVLGKYARLVRSASEGAVC 561


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: 1264
Number of extensions: 60
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: 562
Length adjustment: 36
Effective length of query: 539
Effective length of database: 526
Effective search space:   283514
Effective search space used:   283514
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_005454119.1 SACCYDRAFT_RS04825 (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.11893.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-219  716.3   1.0   1.4e-219  716.1   1.0    1.0  1  lcl|NCBI__GCF_000244975.1:WP_005454119.1  SACCYDRAFT_RS04825 dihydroxy-aci


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000244975.1:WP_005454119.1  SACCYDRAFT_RS04825 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  716.1   1.0  1.4e-219  1.4e-219       2     541 ..      28     561 ..      27     562 .] 0.99

  Alignments for each domain:
  == domain 1  score: 716.1 bits;  conditional E-value: 1.4e-219
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               ara+l+a+G+ d+d+ kP+++v++s++ei+P++++l+ la++ k++++a Gg + ef+t++vsDGi+mg
  lcl|NCBI__GCF_000244975.1:WP_005454119.1  28 ARAMLRAVGMGDADFAKPQVGVASSWNEITPCNLSLRRLAEASKQGVHAGGGYPLEFGTLSVSDGISMG 96 
                                               79******************************************************************* PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               heGm++sL+sre+iaDsvetv++a++lD+ v+++ CDk +PGmlmaa+rl++ a++v+ G+  +g++  
  lcl|NCBI__GCF_000244975.1:WP_005454119.1  97 HEGMHFSLVSREVIADSVETVLEAERLDGAVLLAGCDKSLPGMLMAAARLDVAAVFVYAGSTLPGRLD- 164
                                               ********************************************************************. PP

                                 TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208
                                               +++++++d+feavg+++ g +s e+++++er  cP+ g+C+G++tan+mac++ealG++lPgs++ +++
  lcl|NCBI__GCF_000244975.1:WP_005454119.1 165 GRELTIIDAFEAVGACSRGLMSREDVDRVERAVCPGEGACGGMYTANTMACAAEALGMALPGSASPPSV 233
                                               9******************************************************************** PP

                                 TIGR00110 209 saekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsldd 277
                                               + ++  +a+ sg+ +v l+++ i+ rd+lt+eafenai++++alGGstn+vLhllaia+ea+v lsldd
  lcl|NCBI__GCF_000244975.1:WP_005454119.1 234 DRRRDGFARASGEAVVGLLRRGITARDVLTREAFENAIAVVMALGGSTNAVLHLLAIAHEAEVALSLDD 302
                                               ********************************************************************* PP

                                 TIGR00110 278 fdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrvd 346
                                               f r+ ++vP+la++kP g++v++ ++r+GGv+ v+k l  +g+lh d+ltvtG+t+ae+l+++   ++d
  lcl|NCBI__GCF_000244975.1:WP_005454119.1 303 FSRVGDRVPHLADVKPFGRHVMTAVDRVGGVPVVMKALLDAGHLHGDCLTVTGRTVAENLAEAAPPELD 371
                                               ****************************************************************999** PP

                                 TIGR00110 347 qdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGd 415
                                                 vir+l++p++ +gg+ +L+G la+eGavvk ag +   ++feG+a+vf+ e++a++a+   ++++Gd
  lcl|NCBI__GCF_000244975.1:WP_005454119.1 372 GTVIRELSDPIHPTGGVTILHGTLAPEGAVVKSAGFDR--TRFEGRARVFDGEQAAMAALP--ELSAGD 436
                                               **************************************..*******************96..799*** PP

                                 TIGR00110 416 vvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialved 484
                                               vvviryeGP+GgPGmremLa t a++g+GLg++v L+tDGrfsGgt+Gl+iGhv+Peaa+gG+ia+v+d
  lcl|NCBI__GCF_000244975.1:WP_005454119.1 437 VVVIRYEGPRGGPGMREMLAVTGAIKGAGLGRDVLLLTDGRFSGGTTGLCIGHVAPEAAHGGPIAFVRD 505
                                               ********************************************************************* PP

                                 TIGR00110 485 GDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541
                                               GD i +D+++r+ldl v+++ela+rr+ +++++  e +g+L kya+lv+sa++Gav 
  lcl|NCBI__GCF_000244975.1:WP_005454119.1 506 GDPIVVDLSSRTLDLLVEDAELARRRDGWSPPG-IEHRGVLGKYARLVRSASEGAVC 561
                                               *********************************.679******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (562 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: 10.19
//
[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