Alignments for a candidate for ilvD in Desulfotomaculum ruminis DSM 2154

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Desulfotomaculum ruminis DSM 2154

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_013842410.1 DESRU_RS12190 dihydroxy-acid dehydratase

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



>NCBI__GCF_000215085.1:WP_013842410.1
          Length = 553

 Score =  557 bits (1435), Expect = e-163
 Identities = 280/539 (51%), Positives = 375/539 (69%), Gaps = 3/539 (0%)

Query: 13  APHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEGVNAAGGVAFEFN 72
           A +RSL    G TD+D +KP + + NS+ ++VPGH +LRE++EAVK G+  AGG   EF 
Sbjct: 15  ALNRSLYKSMGYTDEDLDKPLVAVVNSWNNVVPGHYNLREVSEAVKAGIREAGGTPVEFG 74

Query: 73  TMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCDKIVPGMLMAAAR 132
           T+A CDGIA  H+GM+Y L +R+++A+ +E M  AH  DG+VLL +CDKIVPGMLMAAAR
Sbjct: 75  TIAACDGIAQGHEGMRYILPTRDLIANDIEMMIQAHRFDGMVLLGSCDKIVPGMLMAAAR 134

Query: 133 LDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEELERCACPGPRSCA 192
           LD+PAI V GGPMLPG F+G+  D   V E +G + AGEM+  E +ELE CACPGP SCA
Sbjct: 135 LDLPAIFVNGGPMLPGHFQGKDTDSSIVQESLGALKAGEMTLAEYKELENCACPGPGSCA 194

Query: 193 GLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQENLKPTMIMSQE 252
            L TANTM CL EA+GM+LPG +T  AV + + + A+ SG+ IV++++  +    I+++E
Sbjct: 195 MLGTANTMCCLAEAMGMALPGSSTIPAVDASRFRAAQQSGRVIVDLIKRGITAGQIITKE 254

Query: 253 AFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPHIASISPAGEHMM 312
           +  NAV V  A+GGSTN  LHIPAIA E   ++ +L+ F ELS+  PHIA I PA E+ +
Sbjct: 255 SLANAVRVSSAIGGSTNVALHIPAIAYEAK-VDYDLEWFHELSQGTPHIAGIMPASEYDL 313

Query: 313 LDLDRAGGIPAVLKTLEDHINRECVTCTGRTVQENIENVKVGHRDVIRPLDSPVHSEGGL 372
            D   AGG+PAV+K L   +N  C+T TG+TV EN++   +    VI+ +  P H  GGL
Sbjct: 314 ADFHVAGGVPAVMKELAPVLNTNCLTVTGKTVLENVQTAVIKDSRVIKTMSEPFHENGGL 373

Query: 373 AILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGGRIDEGDVIVIRYEG 432
           A+++GNLAP G+V K  A+A +++   GPA+VF+SE   +EAI  G+I  GDV+VIRYEG
Sbjct: 374 AVIKGNLAPNGAVTKPAAIAAELLKFCGPARVFDSEQLAIEAIEAGKIQPGDVVVIRYEG 433

Query: 433 PKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTRGPCVGHVSPEAMEDGPLAAVN 491
           PKGGPGM EM  P   + GMGL ++VALITDGRFSG   G  VGH+SPEAME GPLA V 
Sbjct: 434 PKGGPGMPEMFKPMKLLVGMGLAKKVALITDGRFSGSNNGCFVGHISPEAMEGGPLALVQ 493

Query: 492 DGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPR-RSVKGWLARYRKLAGSADTGAVLR 549
           +GD I IDIP+R+L + +SP E+  R +    P  R  +G+LA Y ++  SAD GA++R
Sbjct: 494 EGDSIDIDIPNRQLNIAISPTELAVRQEKWQAPAPRVTRGYLALYARITESADKGAIIR 552


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: 982
Number of extensions: 44
Number of successful extensions: 4
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: 553
Length adjustment: 36
Effective length of query: 513
Effective length of database: 517
Effective search space:   265221
Effective search space used:   265221
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_013842410.1 DESRU_RS12190 (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.18664.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.9e-223  728.2   3.2   3.3e-223  728.0   3.2    1.0  1  lcl|NCBI__GCF_000215085.1:WP_013842410.1  DESRU_RS12190 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000215085.1:WP_013842410.1  DESRU_RS12190 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  728.0   3.2  3.3e-223  3.3e-223       2     542 ..      17     552 ..      16     553 .] 0.99

  Alignments for each domain:
  == domain 1  score: 728.0 bits;  conditional E-value: 3.3e-223
                                 TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 
                                               +r+l+k++G++dedl+kP++avvns++++vPgh +l++++++vk++i++aGg+++ef+tia +DGia g
  lcl|NCBI__GCF_000215085.1:WP_013842410.1  17 NRSLYKSMGYTDEDLDKPLVAVVNSWNNVVPGHYNLREVSEAVKAGIREAGGTPVEFGTIAACDGIAQG 85 
                                               79******************************************************************* PP

                                 TIGR00110  71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139
                                               heGm+y Lp+r++ia+ +e++++ah++D++v+++sCDkivPGmlmaa+rl++Pai+v GGpm +g+++ 
  lcl|NCBI__GCF_000215085.1:WP_013842410.1  86 HEGMRYILPTRDLIANDIEMMIQAHRFDGMVLLGSCDKIVPGMLMAAARLDLPAIFVNGGPMLPGHFQ- 153
                                               ********************************************************************. PP

                                 TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208
                                               +++ d + v e++g+ +ag+++ +e +e+e++acP++gsC+ l tan+m cl+ea+G++lPgsst++a+
  lcl|NCBI__GCF_000215085.1:WP_013842410.1 154 GKDTDSSIVQESLGALKAGEMTLAEYKELENCACPGPGSCAMLGTANTMCCLAEAMGMALPGSSTIPAV 222
                                               9******************************************************************** PP

                                 TIGR00110 209 saekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsldd 277
                                               +a + + a++sg+ iv+l+k+ i+  +i+tke++ na+ +  a+GGstn  Lh++aia ea+v+++l+ 
  lcl|NCBI__GCF_000215085.1:WP_013842410.1 223 DASRFRAAQQSGRVIVDLIKRGITAGQIITKESLANAVRVSSAIGGSTNVALHIPAIAYEAKVDYDLEW 291
                                               ********************************************************************* PP

                                 TIGR00110 278 fdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrvd 346
                                               f++ls+ +P++a + P++++ ++d h aGGv+av+kel  + +l++++ltvtGkt+ e+++++ ++  d
  lcl|NCBI__GCF_000215085.1:WP_013842410.1 292 FHELSQGTPHIAGIMPASEYDLADFHVAGGVPAVMKEL--APVLNTNCLTVTGKTVLENVQTAVIK--D 356
                                               **************************************..9*********************9999..* PP

                                 TIGR00110 347 qdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGd 415
                                               + vi+++++p++++gglav+kGnla++Gav k a+++ ++lkf Gpa+vf+se+ a+eai +gk++ Gd
  lcl|NCBI__GCF_000215085.1:WP_013842410.1 357 SRVIKTMSEPFHENGGLAVIKGNLAPNGAVTKPAAIAAELLKFCGPARVFDSEQLAIEAIEAGKIQPGD 425
                                               ********************************************************************* PP

                                 TIGR00110 416 vvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialved 484
                                               vvviryeGPkGgPGm+em++P   lvg+GL kkvaLitDGrfsG+ +G  +Gh+sPea+egG++alv++
  lcl|NCBI__GCF_000215085.1:WP_013842410.1 426 VVVIRYEGPKGGPGMPEMFKPMKLLVGMGLAKKVALITDGRFSGSNNGCFVGHISPEAMEGGPLALVQE 494
                                               ********************************************************************* PP

                                 TIGR00110 485 GDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               GD i iDi+nr+l++++s  ela r++k++++ +r ++g+La ya++ +sadkGa+++
  lcl|NCBI__GCF_000215085.1:WP_013842410.1 495 GDSIDIDIPNRQLNIAISPTELAVRQEKWQAPAPRVTRGYLALYARITESADKGAIIR 552
                                               *******************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (553 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: 11.14
//
[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