Alignments for a candidate for ilvD in Steroidobacter denitrificans DSM 18526

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Steroidobacter denitrificans DSM 18526

Align Dihydroxy-acid dehydratase, mitochondrial; DAD; EC 4.2.1.9 (characterized)
to candidate WP_083536603.1 ACG33_RS08125 dihydroxy-acid dehydratase

Query= SwissProt::P39522
         (585 letters)



>NCBI__GCF_001579945.1:WP_083536603.1
          Length = 601

 Score =  570 bits (1469), Expect = e-167
 Identities = 291/560 (51%), Positives = 387/560 (69%), Gaps = 11/560 (1%)

Query: 25  KYSYIITEPKGQGASQAMLYATGFKKEDFKKPQVGVGSCWWSGNPCNMHLLDLNNRCSQS 84
           +YS  + +   Q  S+AML A G+   DFKKP +G+ S W +  PCNMH+  L    + +
Sbjct: 43  RYSSEVVDGLKQTPSRAMLRAVGYTDADFKKPAIGIASTWSNLTPCNMHIDRLARAAAAA 102

Query: 85  IEKAGLKAMQFNTIGVSDGISMGTKGMRYSLQSREIIADSFETIMMAQHYDANIAIPSCD 144
           ++++G KA  F TI VSDGI+ G  GMRYSL SRE+IADS ET+  AQ +D  +AI  CD
Sbjct: 103 VDRSGGKATTFGTITVSDGITNGAPGMRYSLVSREVIADSIETVTGAQGFDGIVAIGGCD 162

Query: 145 KNMPGVMMAMGRHNRPSIMVYGGTILPGHPTCGSSKISKNIDIVSAFQSYGEYISKQFTE 204
           KNMPG MMA+ R +RP++ VYGGTI PG          K+ DI+S F++ G + S   + 
Sbjct: 163 KNMPGCMMALARLDRPAVFVYGGTIRPG---------PKHRDIISVFEARGAFASGAISA 213

Query: 205 EEREDVVEHACPGPGSCGGMYTANTMASAAEVLGLTIPNSSSFPAVSKEKLAECDNIGEY 264
            E +++   A PG GSC GMYTANTMASA E LG+++PNSS+  AVS+ K+ +C+  G+ 
Sbjct: 214 RELKEIECTAIPGAGSCAGMYTANTMASAIEALGMSLPNSSAQEAVSRTKIKDCEAAGKA 273

Query: 265 IKKTMELGILPRDILTKEAFENAITYVVATGGSTNAVLHLVAVAHSAGVKLSPDDFQRIS 324
           + K  +LGI P  IL+++AFENAIT V+A  GSTNAVLHL+A+AH+AG+ L  DDF RI 
Sbjct: 274 VVKLTKLGITPSQILSRKAFENAITVVIALSGSTNAVLHLLAMAHAAGIPLELDDFTRIG 333

Query: 325 DTTPLIGDFKPSGKYVMADLINVGGTQSVIKYLYENNMLHGNTMTVTGDTLAERAKKAPS 384
              P++ D +PSG+Y+M++LI +GG Q ++K L +  +LHG+ +TVTG TL E  +K   
Sbjct: 334 KHVPVLADLRPSGQYMMSELIRIGGIQPLMKMLLDRGLLHGDCLTVTGKTLGENLRKVKP 393

Query: 385 LPEGQEIIKPLSHPIKANGHLQILYGSLAPGGAVGKITGKEGTYFKGRARVFEEEGAFIE 444
            P+ Q+II+  + PIK + HL ILYG+LAP GAV KITGKEG  F GRARVF+ E   ++
Sbjct: 394 YPKNQDIIRAFADPIKPDSHLVILYGNLAPEGAVAKITGKEGLSFTGRARVFDGEEKSVQ 453

Query: 445 ALERGEIKKGEKTVVVIRYEGPRGAPGMPEMLKPSSALMGYGLGKDVALLTDGRFSGGSH 504
           A+  GE++ GE  VVVIRYEGP+G PGM EML P+SAL G GL   VAL+TDGRFSGGS 
Sbjct: 454 AILDGEVQAGE--VVVIRYEGPKGGPGMREMLSPTSALAGIGLIDKVALITDGRFSGGSR 511

Query: 505 GFLIGHIVPEAAEGGPIGLVRDGDEIIIDADNNKIDLLVSDKEMAQRKQSWVAPPPRYTR 564
           GF++GH+ PEAA GG + LV DGDEI IDA   +I L V    + +R+++W APPP   R
Sbjct: 512 GFVVGHMAPEAAVGGTLALVEDGDEITIDAQTREIHLNVPQSVLDRRRKTWQAPPPYTRR 571

Query: 565 GTLSKYAKLVSNASNGCVLD 584
           G L+KYA++VS+AS G V D
Sbjct: 572 GVLAKYARVVSSASLGAVTD 591


Lambda     K      H
   0.315    0.134    0.390 

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: 956
Number of extensions: 46
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: 585
Length of database: 601
Length adjustment: 37
Effective length of query: 548
Effective length of database: 564
Effective search space:   309072
Effective search space used:   309072
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 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate WP_083536603.1 ACG33_RS08125 (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.12671.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.2e-225  734.0   2.8   6.1e-225  733.8   2.8    1.0  1  lcl|NCBI__GCF_001579945.1:WP_083536603.1  ACG33_RS08125 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001579945.1:WP_083536603.1  ACG33_RS08125 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  733.8   2.8  6.1e-225  6.1e-225       1     542 [.      56     591 ..      56     592 .. 0.99

  Alignments for each domain:
  == domain 1  score: 733.8 bits;  conditional E-value: 6.1e-225
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++ra+l+a+G++d+d++kP i++++++++++P+++h++ la++++++++++Gg+a+ f+ti+vsDGi+ 
  lcl|NCBI__GCF_001579945.1:WP_083536603.1  56 PSRAMLRAVGYTDADFKKPAIGIASTWSNLTPCNMHIDRLARAAAAAVDRSGGKATTFGTITVSDGITN 124
                                               589****************************************************************** PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               g  Gm+ysL+sre+iaDs+etv  a+ +D++v+i+ CDk++PG +ma +rl++Pa++v+GG++ +g  +
  lcl|NCBI__GCF_001579945.1:WP_083536603.1 125 GAPGMRYSLVSREVIADSIETVTGAQGFDGIVAIGGCDKNMPGCMMALARLDRPAVFVYGGTIRPGPKH 193
                                               ******************************************************************877 PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                    d+++vfea g+ a+g +s  el+eie +a P+agsC+G++tan+ma++ ealG+slP+ss+ +a
  lcl|NCBI__GCF_001579945.1:WP_083536603.1 194 ----RDIISVFEARGAFASGAISARELKEIECTAIPGAGSCAGMYTANTMASAIEALGMSLPNSSAQEA 258
                                               ....5899************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                               +s  k + ++ +gk +v+l+k  i+P++il+++afenait+++al Gstn+vLhlla+a+ ag+ l+ld
  lcl|NCBI__GCF_001579945.1:WP_083536603.1 259 VSRTKIKDCEAAGKAVVKLTKLGITPSQILSRKAFENAITVVIALSGSTNAVLHLLAMAHAAGIPLELD 327
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345
                                               df r+ ++vP+la+l+Psg++++ +l r GG++ ++k+l  +gllh d+ltvtGktl+e+l kvk  ++
  lcl|NCBI__GCF_001579945.1:WP_083536603.1 328 DFTRIGKHVPVLADLRPSGQYMMSELIRIGGIQPLMKMLLDRGLLHGDCLTVTGKTLGENLRKVKPYPK 396
                                               ********************************************************************* PP

                                 TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                               +qd+ir+  +p+k +++l +L+Gnla+eGav+ki+g+e   l f+G+a+vf+ ee+ ++ail+g+v++G
  lcl|NCBI__GCF_001579945.1:WP_083536603.1 397 NQDIIRAFADPIKPDSHLVILYGNLAPEGAVAKITGKEG--LSFTGRARVFDGEEKSVQAILDGEVQAG 463
                                               ***************************************..9*************************** PP

                                 TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483
                                               +vvviryeGPkGgPGmremL Ptsal+g+GL +kvaLitDGrfsGg+rG+++Gh++Peaa+gG++alve
  lcl|NCBI__GCF_001579945.1:WP_083536603.1 464 EVVVIRYEGPKGGPGMREMLSPTSALAGIGLIDKVALITDGRFSGGSRGFVVGHMAPEAAVGGTLALVE 532
                                               ********************************************************************* PP

                                 TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               dGD+i+iD++ r+++l+v +  l++rr++++++ + + +g+Lakya++vssa+ Gav+d
  lcl|NCBI__GCF_001579945.1:WP_083536603.1 533 DGDEITIDAQTREIHLNVPQSVLDRRRKTWQAPPPYTRRGVLAKYARVVSSASLGAVTD 591
                                               *********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (601 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: 13.64
//
[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