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.16529.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 13.00
//
[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:

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:

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:

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:

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