Alignments for a candidate for ilvD in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Pedobacter sp. GW460-11-11-14-LB5

Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate CA265_RS15795 CA265_RS15795 dihydroxy-acid dehydratase

Query= BRENDA::Q9LIR4
         (608 letters)



>FitnessBrowser__Pedo557:CA265_RS15795
          Length = 560

 Score =  672 bits (1734), Expect = 0.0
 Identities = 335/559 (59%), Positives = 430/559 (76%), Gaps = 2/559 (0%)

Query: 51  NKLNKYSSRITEPKSQGGSQAILHGVGLSDDDLLKPQIGISSVWYEGNTCNMHLLKLSEA 110
           ++LNKYS   T+  +Q  +QA+L+G+GL+D D+ K Q+GI+S+ Y+GNTCNMHL  L++ 
Sbjct: 2   SELNKYSKTFTQDPTQPAAQAMLYGIGLTDADMAKAQVGIASMGYDGNTCNMHLNDLAKD 61

Query: 111 VKEGVENAGMVGFRFNTIGVSDAISMGTRGMCFSLQSRDLIADSIETVMSAQWYDGNISI 170
           VK+GV    +VG  FNTIGVSD +S GT GM +SL SRD+IADSIET+   Q+YDG ISI
Sbjct: 62  VKKGVWKNDLVGLVFNTIGVSDGMSNGTDGMRYSLVSRDVIADSIETICGGQYYDGIISI 121

Query: 171 PGCDKNMPGTIMAMGRLNRPGIMVYGGTIKPGHFQDKTYDIVSAFQSYGEFVSGSISDEQ 230
           PGCDKNMPG IMAM RL+RP IMVYGGTI PGH++ +  +IVSAF++ G+ + G++S+E 
Sbjct: 122 PGCDKNMPGAIMAMARLDRPSIMVYGGTIAPGHYKGEELNIVSAFEALGQKICGNLSEED 181

Query: 231 RKTVLHHSCPGAGACGGMYTANTMASAIEAMGMSLPYSSSIPAEDPLKLDECRLAGKYLL 290
            + ++ H+CPGAGACGGMYTANTMASAIEA+GMSLPYSSS PA    K  EC  AGKY+ 
Sbjct: 182 YQGIIKHTCPGAGACGGMYTANTMASAIEALGMSLPYSSSNPAISEEKKQECLDAGKYIK 241

Query: 291 ELLKMDLKPRDIITPKSLRNAMVSVMALGGSTNAVLHLIAIARSVGLELTLDDFQKVSDA 350
            LL+ D+KP DI+T K+  NA+ S++ LGGSTNAVLH IA+ +++G+E+T DDFQ++SD 
Sbjct: 242 ILLEKDIKPSDIMTRKAFENAIRSIIILGGSTNAVLHFIAMGKAIGIEITQDDFQRMSDV 301

Query: 351 VPFLADLKPSGKYVMEDIHKIGGTPAVLRYLLELGLMDGDCMTVTGQTLAQNLENVPSLT 410
            P LAD KPSGKY+M+D+H+ GG PAVL+YLL  GL+ GDC+TVTG+T+A+NL +V S+ 
Sbjct: 302 TPVLADFKPSGKYLMQDLHQYGGIPAVLKYLLNEGLLHGDCLTVTGKTVAENLADVKSIM 361

Query: 411 E-GQEIIRPLSNPIKETGHIQILRGDLAPDGSVAKITGKEGLYFSGPALVFEGEESMLAA 469
           +  Q+II+ LS PIK TGH+QIL G+LA  GSVAKI+GKEG  F GPA VF+GE  ++A 
Sbjct: 362 DYDQKIIQKLSEPIKATGHLQILYGNLAEKGSVAKISGKEGEKFEGPARVFDGEHDLIAG 421

Query: 470 ISADPMSFKGTVVVIRGEGPKGGPGMPEMLTPTSAIMGAGLGKECALLTDGRFSGGSHGF 529
           IS+  +   G V+VI+  GP G PGMPEML PTSAI+GAGLGK  AL+TDGRFSGG+HGF
Sbjct: 422 ISSGRVQ-PGDVIVIKNSGPVGAPGMPEMLKPTSAIIGAGLGKSVALITDGRFSGGTHGF 480

Query: 530 VVGHICPEAQEGGPIGLIKNGDIITIDIGKKRIDTQVSPEEMNDRRKKWTAPAYKVNRGV 589
           VVGHI PE+ +GG IGL+++ D I ID     I+ QVS E + +RRK +  PA KV +GV
Sbjct: 481 VVGHITPESYKGGLIGLVEDEDRILIDAVNNIINLQVSDEVIAERRKNYVQPALKVTKGV 540

Query: 590 LYKYIKNVQSASDGCVTDE 608
           LYKY K V  A+ GCVTDE
Sbjct: 541 LYKYAKTVSDAASGCVTDE 559


Lambda     K      H
   0.316    0.135    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: 1113
Number of extensions: 48
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: 608
Length of database: 560
Length adjustment: 36
Effective length of query: 572
Effective length of database: 524
Effective search space:   299728
Effective search space used:   299728
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 CA265_RS15795 CA265_RS15795 (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.18223.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.1e-217  709.8   9.5   1.3e-217  709.6   9.5    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS15795  CA265_RS15795 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS15795  CA265_RS15795 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  709.6   9.5  1.3e-217  1.3e-217       2     542 ..      20     558 ..      19     559 .. 0.99

  Alignments for each domain:
  == domain 1  score: 709.6 bits;  conditional E-value: 1.3e-217
                                  TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                                a+a+l+ +Gl+d+d+ k ++++++   + + +++hl+dlak vk+++ ++  v   fnti+vsDG++ 
  lcl|FitnessBrowser__Pedo557:CA265_RS15795  20 AQAMLYGIGLTDADMAKAQVGIASMGYDGNTCNMHLNDLAKDVKKGVWKNDLVGLVFNTIGVSDGMSN 87 
                                                79****************************************************************** PP

                                  TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagkt 137
                                                g++Gm+ysL+sr++iaDs+et++ ++ +D+++ i+ CDk++PG++ma++rl++P+i+v+GG++++g++
  lcl|FitnessBrowser__Pedo557:CA265_RS15795  88 GTDGMRYSLVSRDVIADSIETICGGQYYDGIISIPGCDKNMPGAIMAMARLDRPSIMVYGGTIAPGHY 155
                                                ******************************************************************** PP

                                  TIGR00110 138 klsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstl 205
                                                k +e++++v++fea+g+   g+lsee+ + i +++cP+ag+C+G++tan+ma++ ealG+slP+ss+ 
  lcl|FitnessBrowser__Pedo557:CA265_RS15795 156 K-GEELNIVSAFEALGQKICGNLSEEDYQGIIKHTCPGAGACGGMYTANTMASAIEALGMSLPYSSSN 222
                                                *.9***************************************************************** PP

                                  TIGR00110 206 latsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvkl 273
                                                +a+s+ekk+ +  +gk+i+ l++k+ikP+di+t++afenai  +++lGGstn+vLh +a+ k +g+++
  lcl|FitnessBrowser__Pedo557:CA265_RS15795 223 PAISEEKKQECLDAGKYIKILLEKDIKPSDIMTRKAFENAIRSIIILGGSTNAVLHFIAMGKAIGIEI 290
                                                ******************************************************************** PP

                                  TIGR00110 274 slddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvk 341
                                                + ddf+r+s+ +P+la++kPsgk++++dlh+ GG++avlk+l +egllh d+ltvtGkt+ae+l++vk
  lcl|FitnessBrowser__Pedo557:CA265_RS15795 291 TQDDFQRMSDVTPVLADFKPSGKYLMQDLHQYGGIPAVLKYLLNEGLLHGDCLTVTGKTVAENLADVK 358
                                                ******************************************************************99 PP

                                  TIGR00110 342 vlr.vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailg 408
                                                +++  dq++i++l++p+k++g+l++L+Gnlae+G+v+ki+g+e    kfeGpa+vf+ e++ +++i +
  lcl|FitnessBrowser__Pedo557:CA265_RS15795 359 SIMdYDQKIIQKLSEPIKATGHLQILYGNLAEKGSVAKISGKEG--EKFEGPARVFDGEHDLIAGISS 424
                                                87325666***********************************9..9********************* PP

                                  TIGR00110 409 gkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaeg 476
                                                g+v+ Gdv+vi+  GP G+PGm+emL+Ptsa++g+GLgk+vaLitDGrfsGgt+G+++Gh++Pe+++g
  lcl|FitnessBrowser__Pedo557:CA265_RS15795 425 GRVQPGDVIVIKNSGPVGAPGMPEMLKPTSAIIGAGLGKSVALITDGRFSGGTHGFVVGHITPESYKG 492
                                                ******************************************************************** PP

                                  TIGR00110 477 GaialvedGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                                G i+lved D+i iD+ n+ ++l+vs+e +aerr++ +++  + +kg+L kyak vs a +G+v+d
  lcl|FitnessBrowser__Pedo557:CA265_RS15795 493 GLIGLVEDEDRILIDAVNNIINLQVSDEVIAERRKNYVQPALKVTKGVLYKYAKTVSDAASGCVTD 558
                                                ****************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (560 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 7.59
//
[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