Alignments for a candidate for ilvD in Bacillus alkalinitrilicus DSM 22532

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Bacillus alkalinitrilicus DSM 22532

Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_078427497.1 BK574_RS03330 dihydroxy-acid dehydratase

Query= BRENDA::Q9LIR4
         (608 letters)



>NCBI__GCF_002019605.1:WP_078427497.1
          Length = 556

 Score =  592 bits (1525), Expect = e-173
 Identities = 298/557 (53%), Positives = 403/557 (72%), Gaps = 3/557 (0%)

Query: 51  NKLNKYSSRITEPKSQGGSQAILHGVGLSDDDLLKPQIGISSVWYEGNTCNMHLLKLSEA 110
           N  +K+ S +    ++  ++A++  +G+ D+D  KP +GI+S W E   CNMH+ +L+  
Sbjct: 3   NNTSKFRSSVFNDINRAPNRAMIRAMGIKDEDFNKPFVGIASTWSEVTPCNMHIDELARK 62

Query: 111 VKEGVENAGMVGFRFNTIGVSDAISMGTRGMCFSLQSRDLIADSIETVMSAQWYDGNISI 170
            K+G  +AG   F FNTI VSD ISMGT GM FSL SR++IADSIETV+ AQ YDG ++I
Sbjct: 63  AKKGALDAGGTPFIFNTITVSDGISMGTEGMRFSLPSREVIADSIETVVGAQNYDGVVAI 122

Query: 171 PGCDKNMPGTIMAMGRLNRPGIMVYGGTIKPGHFQDKTYDIVSAFQSYGEFVSGSISDEQ 230
            GCDKNMPG ++A+GRLN P + VYGGTI+PG+   K  DIVSAF++ G++ +G I  ++
Sbjct: 123 GGCDKNMPGCMIAIGRLNLPAVFVYGGTIRPGNVDGKDIDIVSAFEAVGKYNNGDIDRDE 182

Query: 231 RKTVLHHSCPGAGACGGMYTANTMASAIEAMGMSLPYSSSIPAEDPLKLDECRLAGKYLL 290
              +  H+CPGAG+CGGMYTANTMASAIEAMGMSLP SSS PAE   KL++C  AGK ++
Sbjct: 183 LHKIECHACPGAGSCGGMYTANTMASAIEAMGMSLPGSSSNPAETEEKLEDCIKAGKAVM 242

Query: 291 ELLKMDLKPRDIITPKSLRNAMVSVMALGGSTNAVLHLIAIARSVGLELTLDDFQKVSDA 350
            LL   + P+DI+T K+  NA+  VMALGGSTNAVLHL+A+A +V ++L LDDF+++   
Sbjct: 243 NLLNKGITPKDIMTKKAFENAITVVMALGGSTNAVLHLLALAHTVDVDLNLDDFERIRKK 302

Query: 351 VPFLADLKPSGKYVMEDIHKIGGTPAVLRYLLELGLMDGDCMTVTGQTLAQNLENVPSLT 410
           VP +ADLKPSG+YVME++ +IGG PAV++ LL+ GL+ GDC+TVT  T+ QNL  +  L 
Sbjct: 303 VPHIADLKPSGRYVMENLSEIGGVPAVMKLLLDKGLLHGDCLTVTSNTIEQNLSEIQPLK 362

Query: 411 EGQEIIRPLSNPIKETGHIQILRGDLAPDGSVAKITGKEGLYFSGPALVFEGEESMLAAI 470
           EGQEII    NP +ETG + IL+G+LAPDG++AK++G +    +GPA VF+ E     A+
Sbjct: 363 EGQEII-SFENPKRETGPLVILKGNLAPDGALAKMSGLKIKKITGPARVFDSETDATNAV 421

Query: 471 SADPMSFKGTVVVIRGEGPKGGPGMPEMLTPTSAIMGAGLGKECALLTDGRFSGGSHGFV 530
             + ++  G V+VIR  GPKGGPGM EML+ T+ ++G G G++  L+TDGRFSGG+HG V
Sbjct: 422 LNNEVN-PGDVIVIRYVGPKGGPGMAEMLSITAIVVGKGFGEKVGLITDGRFSGGTHGLV 480

Query: 531 VGHICPEAQEGGPIGLIKNGDIITIDIGKKRIDTQVSPEEMNDRRKKWTAPAYKVNRGVL 590
           VGHI PEAQ GGPI LIK GD+ITID   + +   VSPE++N+R K W+ PA  + RG+L
Sbjct: 481 VGHISPEAQVGGPIALIKEGDMITIDSELQELAVDVSPEDLNERLKDWSPPAQNL-RGIL 539

Query: 591 YKYIKNVQSASDGCVTD 607
            KY ++V SAS G +TD
Sbjct: 540 AKYARSVSSASKGAITD 556


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: 1003
Number of extensions: 42
Number of successful extensions: 4
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: 556
Length adjustment: 36
Effective length of query: 572
Effective length of database: 520
Effective search space:   297440
Effective search space used:   297440
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 WP_078427497.1 BK574_RS03330 (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.22246.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-227  742.3   7.4   1.8e-227  742.1   7.4    1.0  1  lcl|NCBI__GCF_002019605.1:WP_078427497.1  BK574_RS03330 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002019605.1:WP_078427497.1  BK574_RS03330 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  742.1   7.4  1.8e-227  1.8e-227       1     542 [.      20     556 .]      20     556 .] 0.99

  Alignments for each domain:
  == domain 1  score: 742.1 bits;  conditional E-value: 1.8e-227
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++ra+++a+G+kded++kP+++++++++e++P+++h+++la+++k++  +aGg+++ fnti+vsDGi+m
  lcl|NCBI__GCF_002019605.1:WP_078427497.1  20 PNRAMIRAMGIKDEDFNKPFVGIASTWSEVTPCNMHIDELARKAKKGALDAGGTPFIFNTITVSDGISM 88 
                                               68******************************************************************* PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               g+eGm++sLpsre+iaDs+etvv a+ +D++v+i+ CDk++PG ++a  rln+Pa++v+GG++ +g++ 
  lcl|NCBI__GCF_002019605.1:WP_078427497.1  89 GTEGMRFSLPSREVIADSIETVVGAQNYDGVVAIGGCDKNMPGCMIAIGRLNLPAVFVYGGTIRPGNVD 157
                                               ********************************************************************* PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                +++id+v++feavg+y++g+++ +el++ie +acP+agsC+G++tan+ma++ ea+G+slPgss+ +a
  lcl|NCBI__GCF_002019605.1:WP_078427497.1 158 -GKDIDIVSAFEAVGKYNNGDIDRDELHKIECHACPGAGSCGGMYTANTMASAIEAMGMSLPGSSSNPA 225
                                               .9******************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                                ++ek+e + k+gk +++l++k i+P+di+tk+afenait+++alGGstn+vLhlla+a++++v+l+ld
  lcl|NCBI__GCF_002019605.1:WP_078427497.1 226 ETEEKLEDCIKAGKAVMNLLNKGITPKDIMTKKAFENAITVVMALGGSTNAVLHLLALAHTVDVDLNLD 294
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345
                                               df+r+++kvP++a+lkPsg++v+e+l + GGv+av+k l  +gllh d+ltvt +t++++l++++ l++
  lcl|NCBI__GCF_002019605.1:WP_078427497.1 295 DFERIRKKVPHIADLKPSGRYVMENLSEIGGVPAVMKLLLDKGLLHGDCLTVTSNTIEQNLSEIQPLKE 363
                                               *******************************************************************99 PP

                                 TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                               +q++i s +np +++g l +LkGnla++Ga++k++g +  i k++Gpa+vf+se +a +a+l+ +v+ G
  lcl|NCBI__GCF_002019605.1:WP_078427497.1 364 GQEII-SFENPKRETGPLVILKGNLAPDGALAKMSGLK--IKKITGPARVFDSETDATNAVLNNEVNPG 429
                                               *9998.79****************************96..59*************************** PP

                                 TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483
                                               dv+viry GPkGgPGm emL  t+ +vg G+g+kv+LitDGrfsGgt+Gl++Gh+sPea +gG+ial++
  lcl|NCBI__GCF_002019605.1:WP_078427497.1 430 DVIVIRYVGPKGGPGMAEMLSITAIVVGKGFGEKVGLITDGRFSGGTHGLVVGHISPEAQVGGPIALIK 498
                                               ********************************************************************* PP

                                 TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
                                               +GD+i+iD e ++l ++vs e+l+er ++++++  ++ +g+Lakya+ vssa+kGa++d
  lcl|NCBI__GCF_002019605.1:WP_078427497.1 499 EGDMITIDSELQELAVDVSPEDLNERLKDWSPPA-QNLRGILAKYARSVSSASKGAITD 556
                                               *******************************999.88*******************986 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.77
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Protein sequences (fasta format)
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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