GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Clostridium tyrobutyricum FAM22553

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_039651789.1 PN53_RS01900 dihydroxy-acid dehydratase

Query= metacyc::MONOMER-11919
         (549 letters)



>NCBI__GCF_000816635.1:WP_039651789.1
          Length = 552

 Score =  613 bits (1582), Expect = e-180
 Identities = 313/553 (56%), Positives = 417/553 (75%), Gaps = 5/553 (0%)

Query: 1   MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60
           MKSD+IK+GI+ AP R+L+   G T ++ E+P IGI NS  ++V GH+HL E+A+A K G
Sbjct: 1   MKSDSIKKGIKGAPARALMYGMGYTKEEIERPLIGIVNSQNEVVAGHMHLDEIAKAAKLG 60

Query: 61  VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120
           V  AGG   EF  +A+CDGIAM H GMK+SLASRE++AD++E+MA AH  DGLVL+P CD
Sbjct: 61  VAMAGGTPMEFPAIAVCDGIAMGHVGMKFSLASRELIADSIEAMATAHGFDGLVLIPNCD 120

Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180
           K+VPGMLMAAARLDIP++VV+GGPM  G+  G+ +D     E VG  S G+++ED+LEE 
Sbjct: 121 KVVPGMLMAAARLDIPSVVVSGGPMRAGKSNGKVLDFSTCIEQVGACSDGKITEDQLEEE 180

Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240
            + +CPG  SC+GLFTAN+M CLTE LGM LP   TA A +  +RQ+A+ +G  +++ V+
Sbjct: 181 AKKSCPGCGSCSGLFTANSMNCLTEVLGMGLPLNGTALAQTGERRQLAKYAGMYVMDCVK 240

Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300
            N +P+ I+  +AF+NA+ +D+A+ GSTNT LH+PAIA E  G+ ++LDLFDE+S+  P 
Sbjct: 241 NNRRPSDILKLDAFKNAITMDMAMAGSTNTVLHLPAIAHEA-GIKLDLDLFDEISQKTPC 299

Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTLEDH--INRECVTCTGRTVQENIENVKVGHRDV 358
           +  +SP+G+H M DL  AGGIPA++  L     I  + +T TG+T+ E I+   V +RDV
Sbjct: 300 LIKLSPSGKHHMEDLHMAGGIPALMHELSSKGLIAEDSMTVTGKTIGETIKEYNVLNRDV 359

Query: 359 IRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIFGG 418
           IR +D+    +GGLAILRGNLA  G+VVK+ AVA++MMVHEGPA+V+NSE+E ++AIFG 
Sbjct: 360 IRSVDNAYSPKGGLAILRGNLAVDGAVVKESAVAKEMMVHEGPARVYNSEEEAVKAIFGD 419

Query: 419 RIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGLER-VALITDGRFSGGTRGPCVGHV 477
            I++GDVIVIRYEGPKGGPGMREML+PTSAIAGMGL++ VAL+TDGRFSG TRG  +GHV
Sbjct: 420 EINKGDVIVIRYEGPKGGPGMREMLSPTSAIAGMGLDKDVALLTDGRFSGATRGASIGHV 479

Query: 478 SPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSV-KGWLARYR 536
           SPEAME G +  V +GD I IDI ++KLE+ +  +E+EER +  VKP   V KG+LARY 
Sbjct: 480 SPEAMEGGLIGLVEEGDTIFIDIKNKKLELKVDAKELEERKKRYVKPEPKVKKGYLARYG 539

Query: 537 KLAGSADTGAVLR 549
           KL  SA+TGAVL+
Sbjct: 540 KLVTSANTGAVLK 552


Lambda     K      H
   0.319    0.136    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: 956
Number of extensions: 43
Number of successful extensions: 5
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: 549
Length of database: 552
Length adjustment: 36
Effective length of query: 513
Effective length of database: 516
Effective search space:   264708
Effective search space used:   264708
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_039651789.1 PN53_RS01900 (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.17088.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-244  798.7  12.0   1.4e-244  798.5  12.0    1.0  1  NCBI__GCF_000816635.1:WP_039651789.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000816635.1:WP_039651789.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  798.5  12.0  1.4e-244  1.4e-244       1     542 [.      14     552 .]      14     552 .] 1.00

  Alignments for each domain:
  == domain 1  score: 798.5 bits;  conditional E-value: 1.4e-244
                             TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheG 73 
                                           +aral++ +G+++e++e+P+i++vns +e+v gh+hl+++ak++k ++  aGg+++ef  iav+DGiamgh G
  NCBI__GCF_000816635.1:WP_039651789.1  14 PARALMYGMGYTKEEIERPLIGIVNSQNEVVAGHMHLDEIAKAAKLGVAMAGGTPMEFPAIAVCDGIAMGHVG 86 
                                           579********************************************************************** PP

                             TIGR00110  74 mkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlv 146
                                           mk+sL+sre+iaDs+e++++ah +D+lv+i++CDk+vPGmlmaa+rl+iP++vvsGGpm agk + ++ +d +
  NCBI__GCF_000816635.1:WP_039651789.1  87 MKFSLASRELIADSIEAMATAHGFDGLVLIPNCDKVVPGMLMAAARLDIPSVVVSGGPMRAGKSN-GKVLDFS 158
                                           ****************************************************************9.9****** PP

                             TIGR00110 147 dvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakks 219
                                             +e vg++++gk++e++lee  + +cP++gsCsGlftansm+clte+lG+ lP ++t+la + e+++lak +
  NCBI__GCF_000816635.1:WP_039651789.1 159 TCIEQVGACSDGKITEDQLEEEAKKSCPGCGSCSGLFTANSMNCLTEVLGMGLPLNGTALAQTGERRQLAKYA 231
                                           ************************************************************************* PP

                             TIGR00110 220 gkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklk 292
                                           g+++++ vk+n +P+dil  +af+nait+d+a+ GstntvLhl+aia+eag+kl+ld fd++s+k+P+l kl+
  NCBI__GCF_000816635.1:WP_039651789.1 232 GMYVMDCVKNNRRPSDILKLDAFKNAITMDMAMAGSTNTVLHLPAIAHEAGIKLDLDLFDEISQKTPCLIKLS 304
                                           ************************************************************************* PP

                             TIGR00110 293 PsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrvdqdvirsldnpvkkegglav 365
                                           Psgk+ +edlh aGG++a+++el+ +gl+ +d++tvtGkt++et+++++vl  ++dvirs+dn+++ +ggla+
  NCBI__GCF_000816635.1:WP_039651789.1 305 PSGKHHMEDLHMAGGIPALMHELSSKGLIAEDSMTVTGKTIGETIKEYNVL--NRDVIRSVDNAYSPKGGLAI 375
                                           **************************************************9..******************** PP

                             TIGR00110 366 LkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPts 438
                                           L+Gnla +Gavvk ++v+++++++eGpa+v++seeea++ai+g ++++Gdv+viryeGPkGgPGmremL Pts
  NCBI__GCF_000816635.1:WP_039651789.1 376 LRGNLAVDGAVVKESAVAKEMMVHEGPARVYNSEEEAVKAIFGDEINKGDVIVIRYEGPKGGPGMREMLSPTS 448
                                           ************************************************************************* PP

                             TIGR00110 439 alvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerra 511
                                           a++g+GL+k+vaL+tDGrfsG+trG siGhvsPea+egG i+lve+GD+i iDi+n+kl+l+v+ +el+er++
  NCBI__GCF_000816635.1:WP_039651789.1 449 AIAGMGLDKDVALLTDGRFSGATRGASIGHVSPEAMEGGLIGLVEEGDTIFIDIKNKKLELKVDAKELEERKK 521
                                           ************************************************************************* PP

                             TIGR00110 512 kakkkearevkgaLakyaklvssadkGavld 542
                                           + +k+e++ +kg+La+y+klv+sa++Gavl+
  NCBI__GCF_000816635.1:WP_039651789.1 522 RYVKPEPKVKKGYLARYGKLVTSANTGAVLK 552
                                           *****************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (552 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: 00:00:00.01
# Mc/sec: 15.42
//
[ok]

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

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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