Alignments for a candidate for ilvD in Thermovibrio ammonificans HB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Thermovibrio ammonificans HB-1

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_013537292.1 THEAM_RS02735 dihydroxy-acid dehydratase

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



>NCBI__GCF_000185805.1:WP_013537292.1
          Length = 550

 Score =  571 bits (1472), Expect = e-167
 Identities = 295/550 (53%), Positives = 388/550 (70%), Gaps = 6/550 (1%)

Query: 1   MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60
           M+SD + R  ++ P R+L+   GL   D +KP IGI +S+TD+VPGH  +  L   ++ G
Sbjct: 1   MRSDVL-REFEKLPARALMMATGLQRKDIDKPLIGIISSWTDLVPGHADMFSLERFIERG 59

Query: 61  VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120
           V AAGG  F     AICDGIAM H+GM++SL  RE++AD +E +  AH LDG+VLL  CD
Sbjct: 60  VAAAGGTPFIVRVPAICDGIAMGHEGMRFSLPLRELIADAIEDVVNAHQLDGIVLLTACD 119

Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLI-NVYEGVGTVSAGEMSEDELEE 179
           KI PGMLM AAR+++PAIVVT GPML G     ++DL+ + +E +G   AGE++ +EL E
Sbjct: 120 KITPGMLMGAARVNVPAIVVTAGPMLAGRRGKERLDLVTHTFEAIGRYKAGEITLEELLE 179

Query: 180 LERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMV 239
           LE  ACP   SC G+FTANTMACLTEALGMSLP C T+ A  + K++IA  SG++IVE+V
Sbjct: 180 LEGAACPSSGSCQGMFTANTMACLTEALGMSLPYCGTSPAPLAEKKRIAEASGEKIVELV 239

Query: 240 QENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIP 299
           ++N++P  I++ +AF NA+ VDLALGGSTNT LH+PAIA E  G+   + LFD+LSR  P
Sbjct: 240 KKNIRPRDILTPQAFRNAIRVDLALGGSTNTVLHLPAIAHEA-GVPFEIKLFDQLSRETP 298

Query: 300 HIASISPAGEHMMLDLDRAGGIPAVLKTLEDHINRECVTCTGRTVQENIENVKVGHRDVI 359
            I S+ P G+++M DL  AGGIP V+K L D +     T  G  ++E     K+   DVI
Sbjct: 299 KICSMRPGGKYLMEDLHYAGGIPGVMKRLYDKLESN-PTVLGTDIKEIAAAAKIWDDDVI 357

Query: 360 RPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGGR 419
           RP D+P   EGG+AIL GNLAP G+V+KQGAV+E M V  G A+VF+SE+E M+A+  G+
Sbjct: 358 RPTDNPYSPEGGIAILYGNLAPEGAVIKQGAVSEKMKVFTGTARVFDSEEEAMKAVMNGQ 417

Query: 420 IDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTRGPCVGHVS 478
           I  GD+IVIRYEGPKGGPGMREML  T+A+ GMGL E VALITDGRFSGGT GPC+GH+S
Sbjct: 418 IKAGDIIVIRYEGPKGGPGMREMLAVTAAVMGMGLGESVALITDGRFSGGTHGPCIGHIS 477

Query: 479 PEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVKG-WLARYRK 537
           PEA E GP+  V DGD I I++P R+LE+ +S  E++ RL+S    ++ +K  +L +Y K
Sbjct: 478 PEAAEGGPIGVVQDGDKIHINVPERRLELLISEEELQNRLKSFKPKQKEIKSKFLRKYAK 537

Query: 538 LAGSADTGAV 547
           L  SA  GA+
Sbjct: 538 LVTSASKGAI 547


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: 959
Number of extensions: 51
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: 549
Length of database: 550
Length adjustment: 36
Effective length of query: 513
Effective length of database: 514
Effective search space:   263682
Effective search space used:   263682
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_013537292.1 THEAM_RS02735 (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.26062.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.9e-235  766.6   1.6   7.8e-235  766.4   1.6    1.0  1  lcl|NCBI__GCF_000185805.1:WP_013537292.1  THEAM_RS02735 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000185805.1:WP_013537292.1  THEAM_RS02735 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  766.4   1.6  7.8e-235  7.8e-235       1     542 [.      13     549 ..      13     550 .] 0.99

  Alignments for each domain:
  == domain 1  score: 766.4 bits;  conditional E-value: 7.8e-235
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               +aral+ atGl+ +d++kP+i++++s+t++vPgh  +  l + +++++ aaGg+++   + a++DGiam
  lcl|NCBI__GCF_000185805.1:WP_013537292.1  13 PARALMMATGLQRKDIDKPLIGIISSWTDLVPGHADMFSLERFIERGVAAAGGTPFIVRVPAICDGIAM 81 
                                               579****************************************************************** PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               gheGm++sLp re+iaD++e vv+ah+lD++v++++CDki+PGmlm+a+r+n+Paivv+ Gpm ag+  
  lcl|NCBI__GCF_000185805.1:WP_013537292.1  82 GHEGMRFSLPLRELIADAIEDVVNAHQLDGIVLLTACDKITPGMLMGAARVNVPAIVVTAGPMLAGRRG 150
                                               *******************************************************************99 PP

                                 TIGR00110 139 lsekidlv.dvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstll 206
                                                 e++dlv + fea+g+y+ag+++ eel e+e  acP++gsC+G+ftan+macltealG+slP+++t++
  lcl|NCBI__GCF_000185805.1:WP_013537292.1 151 -KERLDLVtHTFEAIGRYKAGEITLEELLELEGAACPSSGSCQGMFTANTMACLTEALGMSLPYCGTSP 218
                                               .5777765279********************************************************** PP

                                 TIGR00110 207 atsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsl 275
                                               a  aekk++a+ sg++ivelvkkni+Prdilt +af nai +dlalGGstntvLhl+aia+eagv +++
  lcl|NCBI__GCF_000185805.1:WP_013537292.1 219 APLAEKKRIAEASGEKIVELVKKNIRPRDILTPQAFRNAIRVDLALGGSTNTVLHLPAIAHEAGVPFEI 287
                                               ********************************************************************* PP

                                 TIGR00110 276 ddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr 344
                                               + fd+lsr++P++++++P+gk+++edlh aGG+++v+k l   ++l+++  tv+G+ ++e+++ +k+  
  lcl|NCBI__GCF_000185805.1:WP_013537292.1 288 KLFDQLSRETPKICSMRPGGKYLMEDLHYAGGIPGVMKRL--YDKLESN-PTVLGTDIKEIAAAAKIW- 352
                                               ****************************************..8899999.8***************99. PP

                                 TIGR00110 345 vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvke 413
                                                d+dvir++dnp++ egg+a+L+Gnla+eGav+k+++v+e++ +f+G+a+vf+seeea++a+++g++k+
  lcl|NCBI__GCF_000185805.1:WP_013537292.1 353 -DDDVIRPTDNPYSPEGGIAILYGNLAPEGAVIKQGAVSEKMKVFTGTARVFDSEEEAMKAVMNGQIKA 420
                                               .******************************************************************** PP

                                 TIGR00110 414 GdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialv 482
                                               Gd++viryeGPkGgPGmremLa t+a++g+GLg++vaLitDGrfsGgt+G++iGh+sPeaaegG+i++v
  lcl|NCBI__GCF_000185805.1:WP_013537292.1 421 GDIIVIRYEGPKGGPGMREMLAVTAAVMGMGLGESVALITDGRFSGGTHGPCIGHISPEAAEGGPIGVV 489
                                               ********************************************************************* PP

                                 TIGR00110 483 edGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               +dGDki+i++++r+l+l +seeel++r ++ k+k+++ ++ +L+kyaklv+sa+kGa++d
  lcl|NCBI__GCF_000185805.1:WP_013537292.1 490 QDGDKIHINVPERRLELLISEEELQNRLKSFKPKQKEIKSKFLRKYAKLVTSASKGAIQD 549
                                               ***********************************99999*****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (550 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.73
//
[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