GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Lentibacillus jeotgali Grbi

Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_010532005.1 ON01_RS15945 dihydroxy-acid dehydratase

Query= metacyc::MONOMER-18815
         (557 letters)



>NCBI__GCF_000224785.1:WP_010532005.1
          Length = 563

 Score =  588 bits (1515), Expect = e-172
 Identities = 290/552 (52%), Positives = 394/552 (71%), Gaps = 2/552 (0%)

Query: 6   RSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADAAIDAI 65
           +SQ  +    R+PNR+M  A+G   E F+KPMVGIA+  S +TPCN  +  LA +A    
Sbjct: 8   KSQVFSDDTMRAPNRAMLRAVGLTDEHFEKPMVGIASTWSEVTPCNIHIDDLAVSAKKGA 67

Query: 66  KASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVIGGCDK 125
           + + A P +F T T+SDG+SMGT+GM+YSL SR++IAD IET    + +D  V IG CDK
Sbjct: 68  REAGATPLIFNTITVSDGISMGTQGMRYSLPSRDLIADSIETVVGAENLDAFVAIGACDK 127

Query: 126 NMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQEDFEGVE 185
           N+PG MIA+A ++VP ++VYGGTI PG+  GKD+ +VS FE VG+   G +  ++ + +E
Sbjct: 128 NIPGCMIAIANSDVPAVFVYGGTIAPGSHNGKDIDLVSVFEGVGKHNNGDIDDQELKNIE 187

Query: 186 KNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLVEAIKQ 245
             ACP  G+CGGMYTANTM+S+ EA+GMSL  S++     +EK    AE+   + + ++Q
Sbjct: 188 CKACPGAGACGGMYTANTMASAVEAMGMSLPGSASNPAESEEKAADCAEAGEAVYKLLEQ 247

Query: 246 DIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRKVPVIC 305
            I P+DI+T+K+ ENA+ ++MA GGSTNA+LH L +AHA  V+ TIDDF RI+ KVP + 
Sbjct: 248 GIYPKDIMTKKAFENAMTVVMALGGSTNAILHLLGMAHAVGVDITIDDFNRIQEKVPHLA 307

Query: 306 NLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTPRADQD 365
           +LKPSGQYV  DLH++GG+  VMK+L +AG LHGDCLT+TG+T+AE L   P     DQ 
Sbjct: 308 DLKPSGQYVMQDLHRSGGVQAVMKLLYEAGYLHGDCLTVTGKTVAENLAEAPSLAE-DQK 366

Query: 366 VILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEAILADK 425
           VI P++     +G L +LKGNLA  GAVAK++G+K    TGPARVF  EQ A +A+  +K
Sbjct: 367 VIAPLDNPKRTDGPLIVLKGNLAPRGAVAKVSGVKVSRHTGPARVFNTEQEATDAVRQNK 426

Query: 426 INAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMVVGHVA 485
           I  GD+LV+RY+GPKGGPGMPEML+ +S ++GKGLGE V  +TDGRFSGGT G+VVGH+A
Sbjct: 427 IQEGDVLVIRYVGPKGGPGMPEMLSVSSLLVGKGLGEKVALLTDGRFSGGTHGLVVGHIA 486

Query: 486 PEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVLAKFSK 545
           PEA  GG IA ++EGD++TID+ +  +  +V++EEL RR+ NW  P P Y +GVL K++ 
Sbjct: 487 PEAQDGGPIAFLKEGDNVTIDSDEKEITADVSEEELERRKQNWSAP-PLYKKGVLGKYAH 545

Query: 546 LASTASKGAVTD 557
             S +SKGAVTD
Sbjct: 546 NVSCSSKGAVTD 557


Lambda     K      H
   0.316    0.133    0.386 

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: 918
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: 557
Length of database: 563
Length adjustment: 36
Effective length of query: 521
Effective length of database: 527
Effective search space:   274567
Effective search space used:   274567
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_010532005.1 ON01_RS15945 (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.670102.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-228  744.9   7.1   2.9e-228  744.7   7.1    1.0  1  NCBI__GCF_000224785.1:WP_010532005.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_010532005.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  744.7   7.1  2.9e-228  2.9e-228       1     542 [.      20     557 ..      20     558 .. 0.99

  Alignments for each domain:
  == domain 1  score: 744.7 bits;  conditional E-value: 2.9e-228
                             TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheG 73 
                                           ++ra+l+a+Gl+de +ekP+++++++++e++P+++h++dla  +k++ ++aG+++  fnti+vsDGi+mg++G
  NCBI__GCF_000224785.1:WP_010532005.1  20 PNRAMLRAVGLTDEHFEKPMVGIASTWSEVTPCNIHIDDLAVSAKKGAREAGATPLIFNTITVSDGISMGTQG 92 
                                           68*********************************************************************** PP

                             TIGR00110  74 mkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlv 146
                                           m+ysLpsr++iaDs+etvv a+ lDa v+i++CDk++PG ++a +  ++Pa++v+GG++++g  + +++idlv
  NCBI__GCF_000224785.1:WP_010532005.1  93 MRYSLPSRDLIADSIETVVGAENLDAFVAIGACDKNIPGCMIAIANSDVPAVFVYGGTIAPGSHN-GKDIDLV 164
                                           ****************************************************************9.9****** PP

                             TIGR00110 147 dvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakks 219
                                           +vfe+vg+ ++g+++++el++ie  acP+ag+C+G++tan+ma++ ea+G+slPgs++ +a s+ek++ + ++
  NCBI__GCF_000224785.1:WP_010532005.1 165 SVFEGVGKHNNGDIDDQELKNIECKACPGAGACGGMYTANTMASAVEAMGMSLPGSASNPAESEEKAADCAEA 237
                                           ************************************************************************* PP

                             TIGR00110 220 gkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklk 292
                                           g+ + +l+++ i P+di+tk+afena+t+++alGGstn++Lhll +a+ +gv++++ddf+r+++kvP+la+lk
  NCBI__GCF_000224785.1:WP_010532005.1 238 GEAVYKLLEQGIYPKDIMTKKAFENAMTVVMALGGSTNAILHLLGMAHAVGVDITIDDFNRIQEKVPHLADLK 310
                                           ************************************************************************* PP

                             TIGR00110 293 PsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrvdqdvirsldnpvkkegglav 365
                                           Psg++v++dlhr+GGv+av+k l+++g+lh d+ltvtGkt+ae+l+++++l +dq+vi++ldnp + +g l v
  NCBI__GCF_000224785.1:WP_010532005.1 311 PSGQYVMQDLHRSGGVQAVMKLLYEAGYLHGDCLTVTGKTVAENLAEAPSLAEDQKVIAPLDNPKRTDGPLIV 383
                                           ************************************************************************* PP

                             TIGR00110 366 LkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPts 438
                                           LkGnla++Gav+k++gv+    +++Gpa+vf+ e+ea +a+ + k++eGdv+viry GPkGgPGm+emL  +s
  NCBI__GCF_000224785.1:WP_010532005.1 384 LKGNLAPRGAVAKVSGVKV--SRHTGPARVFNTEQEATDAVRQNKIQEGDVLVIRYVGPKGGPGMPEMLSVSS 454
                                           *****************87..9*************************************************** PP

                             TIGR00110 439 alvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerra 511
                                            lvg GLg+kvaL+tDGrfsGgt+Gl++Gh++Pea  gG+ia++++GD+++iD +++++  +vseeel++r++
  NCBI__GCF_000224785.1:WP_010532005.1 455 LLVGKGLGEKVALLTDGRFSGGTHGLVVGHIAPEAQDGGPIAFLKEGDNVTIDSDEKEITADVSEEELERRKQ 527
                                           ************************************************************************* PP

                             TIGR00110 512 kakkkearevkgaLakyaklvssadkGavld 542
                                           +++++   ++kg+L kya+ vs ++kGav+d
  NCBI__GCF_000224785.1:WP_010532005.1 528 NWSAPP-LYKKGVLGKYAHNVSCSSKGAVTD 557
                                           ****99.789*******************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (563 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 33.14
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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