GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Caldicellulosiruptor kronotskyensis 2002

Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_013430882.1 CALKRO_RS09920 dihydroxy-acid dehydratase

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



>NCBI__GCF_000166775.1:WP_013430882.1
          Length = 552

 Score =  612 bits (1577), Expect = e-179
 Identities = 308/554 (55%), Positives = 413/554 (74%), Gaps = 9/554 (1%)

Query: 1   MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60
           M+SDT+K+G ++AP RSL    G TD++  +P I + NS+ ++VPGHIHL  +AEAVK G
Sbjct: 1   MRSDTVKKGFEKAPQRSLFKAMGYTDEEIRRPLIAVVNSWNEVVPGHIHLDRIAEAVKAG 60

Query: 61  VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120
           +  AG    EFN + +CDGIAM H GMKYSL +RE++AD++E+M MAH  DG+VL+P CD
Sbjct: 61  IRLAGATPMEFNVIGVCDGIAMGHIGMKYSLITRELIADSIEAMVMAHQFDGMVLIPNCD 120

Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFKGRKVDLINVYEGVGTVSAGEMSEDELEEL 180
           KIVPGMLMAAAR++IPAI+++GGPML G+   +  DL +V+EGVG  SAG++SE++L  L
Sbjct: 121 KIVPGMLMAAARVNIPAILISGGPMLAGKVGDKVCDLNSVFEGVGAYSAGKISEEDLYAL 180

Query: 181 ERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQ 240
           E  ACPG  SC+G+FTANTM CL+E LG++LPG  T  AV + + ++A+++G +IVE+V+
Sbjct: 181 EENACPGCGSCSGMFTANTMNCLSEVLGLALPGNGTIPAVMAARIRLAKMAGMKIVELVE 240

Query: 241 ENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPH 300
           +++KP+ I++ EAFENA+ VD+ALGGSTNT LH+PAIA E+ G+ +NLD+ + +S   P+
Sbjct: 241 KDIKPSDILTVEAFENALAVDMALGGSTNTILHLPAIANEV-GIKLNLDIINAISDRTPN 299

Query: 301 IASISPAGEHMMLDLDRAGGIPAVLKTLED----HINRECVTCTGRTVQENIENVKVGHR 356
           +  +SPAG+H + DL  AGG+ AV+  L      H+N   +T TG+TV ENI++  V + 
Sbjct: 300 LCKLSPAGQHHIEDLYFAGGVQAVMNELSKKGLLHLN--LMTVTGKTVGENIKDANVKNY 357

Query: 357 DVIRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAIF 416
           +VIRP+D+P    GGL I+RGNLAP G+VVK+ AV   +M H GPA+VF S +E  EAI 
Sbjct: 358 NVIRPIDNPYSETGGLVIVRGNLAPDGAVVKKSAVPPKLMKHRGPARVFESGEEVFEAIL 417

Query: 417 GGRIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTRGPCVG 475
            G+I +GDVIVIRYEGPKGGPGMREML+PTSA+AG+GL E VALITDGRFSG TRG C G
Sbjct: 418 KGKIQKGDVIVIRYEGPKGGPGMREMLSPTSALAGVGLIEDVALITDGRFSGATRGACFG 477

Query: 476 HVSPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSV-KGWLAR 534
           HVSPEA E GP+AAV DGD+I IDI ++ L +++   EI+ RL+        V KG+L R
Sbjct: 478 HVSPEAAERGPIAAVQDGDMISIDIENKTLTLEVPEEEIKRRLEILPPFEPKVKKGYLYR 537

Query: 535 YRKLAGSADTGAVL 548
           Y KL  SA TGA+L
Sbjct: 538 YSKLVRSASTGAIL 551


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: 946
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_013430882.1 CALKRO_RS09920 (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.677240.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.9e-252  822.3   6.2     1e-251  822.2   6.2    1.0  1  NCBI__GCF_000166775.1:WP_013430882.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166775.1:WP_013430882.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  822.2   6.2    1e-251    1e-251       1     541 [.      14     551 ..      14     552 .] 0.99

  Alignments for each domain:
  == domain 1  score: 822.2 bits;  conditional E-value: 1e-251
                             TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheG 73 
                                           ++r+l+ka+G++de++ +P+iavvns++e+vPgh+hl+ +a++vk++i+ aG++++efn+i+v+DGiamgh G
  NCBI__GCF_000166775.1:WP_013430882.1  14 PQRSLFKAMGYTDEEIRRPLIAVVNSWNEVVPGHIHLDRIAEAVKAGIRLAGATPMEFNVIGVCDGIAMGHIG 86 
                                           589********************************************************************** PP

                             TIGR00110  74 mkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlv 146
                                           mkysL +re+iaDs+e++v+ah++D++v+i++CDkivPGmlmaa+r+niPai++sGGpm agk+   +  dl 
  NCBI__GCF_000166775.1:WP_013430882.1  87 MKYSLITRELIADSIEAMVMAHQFDGMVLIPNCDKIVPGMLMAAARVNIPAILISGGPMLAGKVG-DKVCDLN 158
                                           ****************************************************************9.78899** PP

                             TIGR00110 147 dvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakks 219
                                           +vfe+vg+y+agk+see+l+++e++acP++gsCsG+ftan+m+cl+e+lGl+lPg++t++a+ a + +lak +
  NCBI__GCF_000166775.1:WP_013430882.1 159 SVFEGVGAYSAGKISEEDLYALEENACPGCGSCSGMFTANTMNCLSEVLGLALPGNGTIPAVMAARIRLAKMA 231
                                           ************************************************************************* PP

                             TIGR00110 220 gkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklk 292
                                           g++ivelv+k+ikP+dilt eafena+++d+alGGstnt+Lhl+aia+e+g+kl+ld ++ +s+++P l+kl+
  NCBI__GCF_000166775.1:WP_013430882.1 232 GMKIVELVEKDIKPSDILTVEAFENALAVDMALGGSTNTILHLPAIANEVGIKLNLDIINAISDRTPNLCKLS 304
                                           ************************************************************************* PP

                             TIGR00110 293 PsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrvdqdvirsldnpvkkegglav 365
                                           P+g++ iedl  aGGv+av++el+k+gllh + +tvtGkt++e++++++v+  +++vir++dnp++++ggl +
  NCBI__GCF_000166775.1:WP_013430882.1 305 PAGQHHIEDLYFAGGVQAVMNELSKKGLLHLNLMTVTGKTVGENIKDANVK--NYNVIRPIDNPYSETGGLVI 375
                                           ***************************************************..******************** PP

                             TIGR00110 366 LkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPts 438
                                           ++Gnla++Gavvk ++v  +++k++Gpa+vfes ee+ eail+gk+++Gdv+viryeGPkGgPGmremL Pts
  NCBI__GCF_000166775.1:WP_013430882.1 376 VRGNLAPDGAVVKKSAVPPKLMKHRGPARVFESGEEVFEAILKGKIQKGDVIVIRYEGPKGGPGMREMLSPTS 448
                                           ************************************************************************* PP

                             TIGR00110 439 alvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerra 511
                                           al+g+GL ++vaLitDGrfsG+trG + GhvsPeaae G+ia v+dGD+i+iDien++l lev eee+++r +
  NCBI__GCF_000166775.1:WP_013430882.1 449 ALAGVGLIEDVALITDGRFSGATRGACFGHVSPEAAERGPIAAVQDGDMISIDIENKTLTLEVPEEEIKRRLE 521
                                           ************************************************************************* PP

                             TIGR00110 512 kakkkearevkgaLakyaklvssadkGavl 541
                                              + e++ +kg+L +y+klv+sa++Ga+l
  NCBI__GCF_000166775.1:WP_013430882.1 522 ILPPFEPKVKKGYLYRYSKLVRSASTGAIL 551
                                           ****************************97 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: 18.95
//
[ok]

This GapMind analysis is from Jul 26 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