Alignments for a candidate for ilvD in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Echinicola vietnamensis KMM 6221, DSM 17526

Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate Echvi_2055 Echvi_2055 dihydroxy-acid dehydratase

Query= BRENDA::A0A481UJA7
         (614 letters)



>FitnessBrowser__Cola:Echvi_2055
          Length = 561

 Score =  644 bits (1660), Expect = 0.0
 Identities = 311/557 (55%), Positives = 414/557 (74%), Gaps = 2/557 (0%)

Query: 59  LNKYSSRITEPKSQGGSQAILHGVGLSDEDLNKPQIGISSVWYEGNTCNMHLLRLSEAVK 118
           L KYS  I++ +    + A+L+  G++D+ + +P +G++S  YE N CNMHL   +E +K
Sbjct: 5   LKKYSWEISDNEENPAAMAMLYATGITDKKMKQPFVGVASCGYESNPCNMHLNSFAEDIK 64

Query: 119 EGVKEAGMVGFRFNTIGVSDAISMGTRGMCYSLQSRDLIADSIETVMSAQWYDGNISIPG 178
               +A + GF FNTIG+SD  SMGT GM YSL SR++IADSIE+ +    +DG ++IPG
Sbjct: 65  ASTNQADLSGFIFNTIGISDGQSMGTSGMRYSLPSREVIADSIESFILGHSFDGVVTIPG 124

Query: 179 CDKNMPGTIMAMGRLNRPSIMVYGGTIKPGHYNGHSYDIISAFQAYGEYVNGSISDEDRK 238
           CDKNMPG +M M R+NRP IMV+GGTI+ G+Y G   +I+SAF+AYG+ +NG ISDED  
Sbjct: 125 CDKNMPGVVMGMLRVNRPGIMVFGGTIRSGNYKGEKLNIVSAFEAYGKKINGQISDEDYM 184

Query: 239 NVVHNSCPGAGACGGMYTANTMASAIEAMGMCLPYSSSIPAENPLKLDECRLAGKYLLEL 298
            V+ N+CPGAGACGGMYTANTM+SAIEAMG+ LP+SSS PA +  K +EC+  GKY+ +L
Sbjct: 185 GVIKNACPGAGACGGMYTANTMSSAIEAMGLSLPFSSSYPATSKEKREECKNIGKYIKQL 244

Query: 299 LKMDLKPQNIITPQSLRNAMVVVMALGGSTNAVLHLIPIARSVGLELTLEDFQKVSDEVP 358
           L +D+KP++IIT +SL NA+ V +ALGGSTNA LH++ IAR+ G++ TLEDF++++ E P
Sbjct: 245 LALDIKPKDIITKKSLENAVRVTVALGGSTNAALHILAIARTAGIDFTLEDFKRINAETP 304

Query: 359 FLADLKPSGKYVMEDVHKIGGTPAVLRYLLEHGFLDGDCLTVTGKTLAENVQNCPPLSEG 418
            L D KPSGK++MED++++GG PA L+Y L  G L GDCLTVTGKT+AEN+++  P+   
Sbjct: 305 VLGDFKPSGKFMMEDLYEMGGLPAFLKYFLNEGLLHGDCLTVTGKTMAENLEDIDPVKPS 364

Query: 419 QD-IIRPLENPIKKTGHIQILQGNLAPEGSVAKITGKEGLYFSGPALVFEGEEAMLAAIS 477
           ++ +I PL+NPIK +GH+ +L GNLAPEG+VAKI+GKEG  F+G A VF+ E +  AA+ 
Sbjct: 365 KESVIHPLDNPIKPSGHLCVLHGNLAPEGAVAKISGKEGKSFTGTAKVFDDEPSANAAMK 424

Query: 478 ENPMNFKGKVVVIRGEGPKGGPGMPEMLTPTSAIMGAGLGKDCALLTDGRFSGGSHGFVV 537
              +  KG VVVIR  GPKGGPGMPEML PTS I+GAGLG D AL+TDGRFSGG+HGFVV
Sbjct: 425 NKEIQ-KGDVVVIRYVGPKGGPGMPEMLKPTSIIIGAGLGSDVALITDGRFSGGTHGFVV 483

Query: 538 GHICPEAQEGGPIGLVRNGDIIRIDVRERRIDVDVTDQEMEERRKNWTPPPYKATCGVLY 597
           GH+ PEA  GGPIGL+++GD+I ID     I VDV++ E  ER+KNW         G L 
Sbjct: 484 GHVTPEAYLGGPIGLLKDGDVITIDAESLEIRVDVSEAEFAERKKNWKNKDLSHLQGTLK 543

Query: 598 KYIKNVQSASRGCVTDE 614
           KY++ V +AS GCVTD+
Sbjct: 544 KYVQLVSTASEGCVTDK 560


Lambda     K      H
   0.316    0.135    0.401 

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: 1060
Number of extensions: 42
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: 614
Length of database: 561
Length adjustment: 37
Effective length of query: 577
Effective length of database: 524
Effective search space:   302348
Effective search space used:   302348
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 Echvi_2055 Echvi_2055 (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.29097.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
     9e-224  729.9   3.6     1e-223  729.7   3.6    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2055  Echvi_2055 dihydroxy-acid dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2055  Echvi_2055 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  729.7   3.6    1e-223    1e-223       2     542 ..      21     559 ..      20     560 .. 0.99

  Alignments for each domain:
  == domain 1  score: 729.7 bits;  conditional E-value: 1e-223
                            TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmk 75 
                                          a a+l+atG++d+ +++P+++v+++  e +P+++hl+ +a+ +k++ ++a    + fnti++sDG +mg++Gm+
  lcl|FitnessBrowser__Cola:Echvi_2055  21 AMAMLYATGITDKKMKQPFVGVASCGYESNPCNMHLNSFAEDIKASTNQADLSGFIFNTIGISDGQSMGTSGMR 94 
                                          579*********************************************************************** PP

                            TIGR00110  76 ysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvdvf 149
                                          ysLpsre+iaDs+e+ + +h +D++v+i+ CDk++PG++m++lr+n+P i+v GG++ +g++k +ek+++v++f
  lcl|FitnessBrowser__Cola:Echvi_2055  95 YSLPSREVIADSIESFILGHSFDGVVTIPGCDKNMPGVVMGMLRVNRPGIMVFGGTIRSGNYK-GEKLNIVSAF 167
                                          ***************************************************************.9********* PP

                            TIGR00110 150 eavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkri 223
                                          ea+g+  +g++s+e+   + ++acP+ag+C+G++tan+m+++ ea+GlslP ss+ +ats+ek+e +k++gk+i
  lcl|FitnessBrowser__Cola:Echvi_2055 168 EAYGKKINGQISDEDYMGVIKNACPGAGACGGMYTANTMSSAIEAMGLSLPFSSSYPATSKEKREECKNIGKYI 241
                                          ************************************************************************** PP

                            TIGR00110 224 velvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkk 297
                                          ++l+  +ikP+di+tk+++ena+ + +alGGstn+ Lh+laia++ag++++l+df+r++ ++P+l+++kPsgk 
  lcl|FitnessBrowser__Cola:Echvi_2055 242 KQLLALDIKPKDIITKKSLENAVRVTVALGGSTNAALHILAIARTAGIDFTLEDFKRINAETPVLGDFKPSGKF 315
                                          ************************************************************************** PP

                            TIGR00110 298 viedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvk.vlrvdqdvirsldnpvkkegglavLkGnl 370
                                          ++edl + GG++a lk+  +egllh d+ltvtGkt+ae+le+++ v++ +++vi++ldnp+k  g+l vL+Gnl
  lcl|FitnessBrowser__Cola:Echvi_2055 316 MMEDLYEMGGLPAFLKYFLNEGLLHGDCLTVTGKTMAENLEDIDpVKPSKESVIHPLDNPIKPSGHLCVLHGNL 389
                                          ******************************************9735667888********************** PP

                            TIGR00110 371 aeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglG 444
                                          a+eGav+ki+g+e     f+G+akvf++e  a +a+ ++++++Gdvvviry GPkGgPGm+emL+Pts ++g+G
  lcl|FitnessBrowser__Cola:Echvi_2055 390 APEGAVAKISGKEG--KSFTGTAKVFDDEPSANAAMKNKEIQKGDVVVIRYVGPKGGPGMPEMLKPTSIIIGAG 461
                                          **************..99******************************************************** PP

                            TIGR00110 445 LgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea 518
                                          Lg++vaLitDGrfsGgt+G+++Ghv+Pea+ gG+i+l++dGD i+iD+e+ ++ ++vse+e+aer++++k+k+ 
  lcl|FitnessBrowser__Cola:Echvi_2055 462 LGSDVALITDGRFSGGTHGFVVGHVTPEAYLGGPIGLLKDGDVITIDAESLEIRVDVSEAEFAERKKNWKNKDL 535
                                          ************************************************************************** PP

                            TIGR00110 519 revkgaLakyaklvssadkGavld 542
                                           + +g+L+ky +lvs+a++G+v+d
  lcl|FitnessBrowser__Cola:Echvi_2055 536 SHLQGTLKKYVQLVSTASEGCVTD 559
                                          **********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (561 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: 9.49
//
[ok]

This GapMind analysis is from Apr 09 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