Alignments for a candidate for ilvD in Desulfatibacillum aliphaticivorans DSM 15576

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Desulfatibacillum aliphaticivorans DSM 15576

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_028314077.1 G491_RS0107060 dihydroxy-acid dehydratase

Query= metacyc::MONOMER-11919
         (549 letters)



>NCBI__GCF_000429905.1:WP_028314077.1
          Length = 556

 Score =  618 bits (1593), Expect = 0.0
 Identities = 310/556 (55%), Positives = 406/556 (73%), Gaps = 9/556 (1%)

Query: 1   MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60
           MKSD ++ G++RAPHRSL    G TD++  +P IG+AN    ++PGH+HL  +AEAV++G
Sbjct: 1   MKSDNVRIGLERAPHRSLFKAMGYTDEELNRPLIGVANPMNAVIPGHVHLNNIAEAVQKG 60

Query: 61  VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120
           +  AGG    F  + +CDGIAMNH GMKYSLASREI+AD+VE MA AHA DGLVL+  CD
Sbjct: 61  IYLAGGTPAIFGGIGVCDGIAMNHAGMKYSLASREIIADSVEIMATAHAFDGLVLICNCD 120

Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEF----KGRKVDLINVYEGVGTVSAGEMSEDE 176
           KIVPGMLMAAAR+DIP ++++GGPML G       G K+DLI V+EGVG V +G+M+E+E
Sbjct: 121 KIVPGMLMAAARIDIPTVIISGGPMLAGSHPNVKNGEKIDLITVFEGVGAVKSGKMTEEE 180

Query: 177 LEELERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIV 236
           L  +E  ACP   SCAG+FTAN+M CLTE +GM LPG  T  AV + + ++A+ +G  I+
Sbjct: 181 LSLMEDEACPTCGSCAGMFTANSMNCLTEVIGMGLPGNGTIPAVMASRIRLAKQAGMAIM 240

Query: 237 EMVQENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSR 296
           +MV++N+ P+ IM+ EAF NA+ VD+ALG STNT LH+PAIA E  G+  +L   +E+S 
Sbjct: 241 DMVEKNITPSQIMTPEAFANALAVDMALGCSTNTALHLPAIAHEA-GVEFDLKQINEISA 299

Query: 297 VIPHIASISPAGEHMMLDLDRAGGIPAVLKTLEDH--INRECVTCTGRTVQENIENVKVG 354
            IPH+  +SP G H + DL+RAGGI AVL  L  H  IN +C+T TG++V EN    ++ 
Sbjct: 300 RIPHLCQLSPGGYHRIEDLNRAGGIQAVLSELIKHNLINTDCITVTGKSVGENASKARIL 359

Query: 355 HRDVIRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEA 414
             +VIR +++P H EGGLA+L GN+AP G VVKQ AV + M+VHEGPA+VF+SEDE  +A
Sbjct: 360 DPEVIRSVETPYHKEGGLAVLFGNVAPEGCVVKQSAVVDKMLVHEGPARVFDSEDEASKA 419

Query: 415 IFGGRIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGLER-VALITDGRFSGGTRGPC 473
           I  G I +GDV+V+RYEGPKGGPGMREML PTS IAGMGL+  VALITDGRFSGGTRG  
Sbjct: 420 IMDGLIKKGDVVVVRYEGPKGGPGMREMLTPTSVIAGMGLDADVALITDGRFSGGTRGAA 479

Query: 474 VGHVSPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSV-KGWL 532
           +GHVSPEAM  GP+AAV +GDII+I+IP + + +D+   EI+ R+     P   + KG++
Sbjct: 480 IGHVSPEAMSGGPIAAVREGDIIKINIPEKTIALDVPEEEIKARMADWTPPEPKITKGYM 539

Query: 533 ARYRKLAGSADTGAVL 548
           ARY +   SA  GAV+
Sbjct: 540 ARYARNVESASKGAVV 555


Lambda     K      H
   0.319    0.136    0.397 

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: 978
Number of extensions: 44
Number of successful extensions: 6
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: 549
Length of database: 556
Length adjustment: 36
Effective length of query: 513
Effective length of database: 520
Effective search space:   266760
Effective search space used:   266760
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_028314077.1 G491_RS0107060 (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.11937.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.5e-243  793.3  14.1   6.2e-243  793.1  14.1    1.0  1  lcl|NCBI__GCF_000429905.1:WP_028314077.1  G491_RS0107060 dihydroxy-acid de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429905.1:WP_028314077.1  G491_RS0107060 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  793.1  14.1  6.2e-243  6.2e-243       1     541 [.      14     555 ..      14     556 .] 0.99

  Alignments for each domain:
  == domain 1  score: 793.1 bits;  conditional E-value: 6.2e-243
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++r+l+ka+G++de+l++P+i+v+n  + ++Pghvhl+++a++v+++i+ aGg++  f+ i+v+DGiam
  lcl|NCBI__GCF_000429905.1:WP_028314077.1  14 PHRSLFKAMGYTDEELNRPLIGVANPMNAVIPGHVHLNNIAEAVQKGIYLAGGTPAIFGGIGVCDGIAM 82 
                                               69******************************************************************* PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagk.. 136
                                               +h GmkysL+sreiiaDsve +++aha+D+lv+i +CDkivPGmlmaa+r++iP++++sGGpm ag   
  lcl|NCBI__GCF_000429905.1:WP_028314077.1  83 NHAGMKYSLASREIIADSVEIMATAHAFDGLVLICNCDKIVPGMLMAAARIDIPTVIISGGPMLAGShp 151
                                               *****************************************************************9622 PP

                                 TIGR00110 137 .tklsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsst 204
                                                +k +ekidl+ vfe+vg++++gk++eeel+ +e+ acPt+gsC+G+ftansm+clte++G+ lPg++t
  lcl|NCBI__GCF_000429905.1:WP_028314077.1 152 nVKNGEKIDLITVFEGVGAVKSGKMTEEELSLMEDEACPTCGSCAGMFTANSMNCLTEVIGMGLPGNGT 220
                                               2567***************************************************************** PP

                                 TIGR00110 205 llatsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvkl 273
                                               ++a+ a + +lak++g+ i+++v+kni+P++i+t eaf na+++d+alG stnt Lhl+aia+eagv++
  lcl|NCBI__GCF_000429905.1:WP_028314077.1 221 IPAVMASRIRLAKQAGMAIMDMVEKNITPSQIMTPEAFANALAVDMALGCSTNTALHLPAIAHEAGVEF 289
                                               ********************************************************************* PP

                                 TIGR00110 274 slddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkv 342
                                               +l++++++s ++P+l++l+P+g + iedl+raGG++avl el k++l+++d++tvtGk+++e+++k+++
  lcl|NCBI__GCF_000429905.1:WP_028314077.1 290 DLKQINEISARIPHLCQLSPGGYHRIEDLNRAGGIQAVLSELIKHNLINTDCITVTGKSVGENASKARI 358
                                               *******************************************************************99 PP

                                 TIGR00110 343 lrvdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkv 411
                                               l  d +virs++ p++kegglavL+Gn+a+eG+vvk+++v +++l++eGpa+vf+se+ea +ai++g +
  lcl|NCBI__GCF_000429905.1:WP_028314077.1 359 L--DPEVIRSVETPYHKEGGLAVLFGNVAPEGCVVKQSAVVDKMLVHEGPARVFDSEDEASKAIMDGLI 425
                                               9..****************************************************************** PP

                                 TIGR00110 412 keGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaia 480
                                               k+Gdvvv+ryeGPkGgPGmremL+Pts+++g+GL+ +vaLitDGrfsGgtrG +iGhvsPea++gG+ia
  lcl|NCBI__GCF_000429905.1:WP_028314077.1 426 KKGDVVVVRYEGPKGGPGMREMLTPTSVIAGMGLDADVALITDGRFSGGTRGAAIGHVSPEAMSGGPIA 494
                                               ********************************************************************* PP

                                 TIGR00110 481 lvedGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541
                                                v++GD+iki+i+++++ l+v eee+++r a+++++e++ +kg++a+ya+ v+sa+kGav+
  lcl|NCBI__GCF_000429905.1:WP_028314077.1 495 AVREGDIIKINIPEKTIALDVPEEEIKARMADWTPPEPKITKGYMARYARNVESASKGAVV 555
                                               ***********************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (556 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: 9.48
//
[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