Alignments for a candidate for ilvD in Kyrpidia tusciae DSM 2912

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Kyrpidia tusciae DSM 2912

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_013075051.1 BTUS_RS05140 dihydroxy-acid dehydratase

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



>NCBI__GCF_000092905.1:WP_013075051.1
          Length = 556

 Score =  592 bits (1526), Expect = e-173
 Identities = 304/555 (54%), Positives = 401/555 (72%), Gaps = 7/555 (1%)

Query: 1   MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60
           M+SD IKRG+ +APHRSLL   G+ D+DF KPFIGI NS+ +I+PGH+HL+E    +KE 
Sbjct: 1   MRSDMIKRGVDKAPHRSLLKATGVRDEDFGKPFIGICNSFVEIIPGHVHLQEFGRLIKEA 60

Query: 61  VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120
           V  AGGV FEFNT+ + DGIAM H GM++SL SRE++AD+VE+MAMAH  DGL+ +P CD
Sbjct: 61  VREAGGVPFEFNTIGVDDGIAMGHIGMRFSLPSRELIADSVETMAMAHWFDGLICIPNCD 120

Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEF-KGRKVDLINVYEGVGTVSAGEMSEDELEE 179
           KI PGMLMAA R++IP I ++GGPM  G    G+ VDLI+V+EGVG   +G++S DEL+E
Sbjct: 121 KITPGMLMAAMRVNIPTIFISGGPMAAGRTPSGKIVDLISVFEGVGAYQSGQISMDELKE 180

Query: 180 LERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMV 239
           LE   CP   SC+G+FTAN+M CL+EALGM+LPG  +  A +  + ++AR +  +I+E+V
Sbjct: 181 LEDYGCPSCGSCSGMFTANSMNCLSEALGMALPGNGSILANTPEREELARKAAIQILELV 240

Query: 240 QENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIP 299
           + +LKP  I++ ++ +NA  +D+A+GGSTNT LH  AIA E  G+   L   DE+SR  P
Sbjct: 241 RRDLKPRDIVTIDSLDNAFALDMAMGGSTNTVLHTLAIAKEA-GVEYPLSRIDEISRRTP 299

Query: 300 HIASISPAGEHMMLDLDRAGGIPAVLKTL---EDHINRECVTCTGRTVQENIENVKVGHR 356
           H+  +SPA    M D+ RAGGI A+LK L   +  ++ + +T TGR++ ENI + ++   
Sbjct: 300 HLCKVSPASHWHMEDVHRAGGISAILKELSRIDGLLHLDAMTVTGRSLGENIADAEIRDP 359

Query: 357 DVIRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIF 416
           +VIRP+++     GGLAIL GNLAP G+V+K GAV E +   EGPA +F S+DE  E I 
Sbjct: 360 EVIRPIENAYSQTGGLAILSGNLAPNGAVIKAGAVDESVKRFEGPAVIFESQDEAFEGIM 419

Query: 417 GGRIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTRGPCVG 475
            G+I EGDV+VIRYEGPKGGPGM EML PTSA+AGMGL  +VALITDGRFSGG+RG  VG
Sbjct: 420 SGKIHEGDVVVIRYEGPKGGPGMPEMLAPTSALAGMGLGAKVALITDGRFSGGSRGISVG 479

Query: 476 HVSPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVK-GWLAR 534
           H+SPEA E GP+A + DGD++ IDIP RKLEV L+  E+ ER      P   V+ G+LAR
Sbjct: 480 HISPEAAEGGPIALLQDGDMVVIDIPGRKLEVKLTDEELAERRAKWRAPEPKVRTGYLAR 539

Query: 535 YRKLAGSADTGAVLR 549
           Y KL  SA+TGAVL+
Sbjct: 540 YAKLVTSANTGAVLK 554


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: 981
Number of extensions: 57
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_013075051.1 BTUS_RS05140 (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.20740.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.1e-266  870.1   0.9   3.5e-266  869.9   0.9    1.0  1  lcl|NCBI__GCF_000092905.1:WP_013075051.1  BTUS_RS05140 dihydroxy-acid dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092905.1:WP_013075051.1  BTUS_RS05140 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  869.9   0.9  3.5e-266  3.5e-266       1     542 [.      14     554 ..      14     555 .. 1.00

  Alignments for each domain:
  == domain 1  score: 869.9 bits;  conditional E-value: 3.5e-266
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++r+llkatG++ded++kP+i+++ns++ei+Pghvhl+++++l+ke++++aGgv++efnti+v+DGiam
  lcl|NCBI__GCF_000092905.1:WP_013075051.1  14 PHRSLLKATGVRDEDFGKPFIGICNSFVEIIPGHVHLQEFGRLIKEAVREAGGVPFEFNTIGVDDGIAM 82 
                                               69******************************************************************* PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               gh Gm++sLpsre+iaDsvet+++ah++D+l++i++CDki+PGmlmaa+r+niP+i++sGGpm+ag+t 
  lcl|NCBI__GCF_000092905.1:WP_013075051.1  83 GHIGMRFSLPSRELIADSVETMAMAHWFDGLICIPNCDKITPGMLMAAMRVNIPTIFISGGPMAAGRTP 151
                                               ********************************************************************* PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                ++ +dl++vfe+vg+y++g++s +el+e+e+++cP++gsCsG+ftansm+cl+ealG++lPg++++la
  lcl|NCBI__GCF_000092905.1:WP_013075051.1 152 SGKIVDLISVFEGVGAYQSGQISMDELKELEDYGCPSCGSCSGMFTANSMNCLSEALGMALPGNGSILA 220
                                               ********************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                                + e++ela+k++ +i elv++++kPrdi+t ++++na++ld+a+GGstntvLh+laiakeagv++ l+
  lcl|NCBI__GCF_000092905.1:WP_013075051.1 221 NTPEREELARKAAIQILELVRRDLKPRDIVTIDSLDNAFALDMAMGGSTNTVLHTLAIAKEAGVEYPLS 289
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldk.egllhkdaltvtGktlaetlekvkvlr 344
                                               ++d++sr++P+l+k++P+++  +ed+hraGG+sa+lkel++ +gllh da+tvtG++l+e++++++++ 
  lcl|NCBI__GCF_000092905.1:WP_013075051.1 290 RIDEISRRTPHLCKVSPASHWHMEDVHRAGGISAILKELSRiDGLLHLDAMTVTGRSLGENIADAEIR- 357
                                               ****************************************9899************************. PP

                                 TIGR00110 345 vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvke 413
                                                d +vir+++n+++++ggla+L Gnla++Gav+k+++v+e++ +feGpa +fes++ea e+i++gk++e
  lcl|NCBI__GCF_000092905.1:WP_013075051.1 358 -DPEVIRPIENAYSQTGGLAILSGNLAPNGAVIKAGAVDESVKRFEGPAVIFESQDEAFEGIMSGKIHE 425
                                               .******************************************************************** PP

                                 TIGR00110 414 GdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialv 482
                                               GdvvviryeGPkGgPGm+emLaPtsal+g+GLg kvaLitDGrfsGg+rG+s+Gh+sPeaaegG+ial+
  lcl|NCBI__GCF_000092905.1:WP_013075051.1 426 GDVVVIRYEGPKGGPGMPEMLAPTSALAGMGLGAKVALITDGRFSGGSRGISVGHISPEAAEGGPIALL 494
                                               ********************************************************************* PP

                                 TIGR00110 483 edGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               +dGD++ iDi+ rkl++++ +eelaerrak++++e++   g+La+yaklv+sa++Gavl+
  lcl|NCBI__GCF_000092905.1:WP_013075051.1 495 QDGDMVVIDIPGRKLEVKLTDEELAERRAKWRAPEPKVRTGYLARYAKLVTSANTGAVLK 554
                                               **********************************************************97 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: 10.00
//
[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