GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuA in Streptacidiphilus oryzae TH49

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_037576554.1 BS73_RS26265 2-isopropylmalate synthase

Query= BRENDA::P9WQB3
         (644 letters)



>NCBI__GCF_000744815.1:WP_037576554.1
          Length = 582

 Score =  665 bits (1715), Expect = 0.0
 Identities = 351/617 (56%), Positives = 429/617 (69%), Gaps = 58/617 (9%)

Query: 36  QRASSMPVNRYRPFAEEVEPIRLRNRTWPDRVIDRAPLWCAVDLRDGNQALIDPMSPARK 95
           Q+ S MP  RY+PF      + L +RTWP +VI +AP W + DLRDGNQALIDPMSPARK
Sbjct: 14  QKPSGMPFQRYKPFGT----VDLPDRTWPGKVITKAPRWLSTDLRDGNQALIDPMSPARK 69

Query: 96  RRMFDLLVRMGYKEIEVGFPSASQTDFDFVREIIEQGAIPDDVTIQVLTQCRPELIERTF 155
           R MFDLLVR+GYKEIEVGFPS+ QTDFDFVR IIE+GAIP+DVTI VLTQ R +LIERT 
Sbjct: 70  RAMFDLLVRLGYKEIEVGFPSSGQTDFDFVRSIIEEGAIPEDVTISVLTQAREDLIERTV 129

Query: 156 QACSGAPRAIVHFYNSTSILQRRVVFRANRAEVQAIATDGARKCVEQAAKYPG--TQWRF 213
           ++  GAPRA VH YN+T+ L RRVVFRA+R EV+ IA DG    ++ A +  G  T + +
Sbjct: 130 ESLVGAPRATVHMYNATAPLFRRVVFRASRDEVRQIAVDGTGHVMKYAEQLLGEDTVFGY 189

Query: 214 EYSPESYTGTELEYAKQVCDAVGEVIAPTPERPIIFNLPATVEMTTPNVYADSIEWMSRN 273
           +YSPE +  TEL++A +VC+AV +V  P   R II NLP TVE  TPNVYAD IEWMSRN
Sbjct: 190 QYSPEIFVDTELDFALEVCEAVMDVWQPEEGREIILNLPTTVERCTPNVYADQIEWMSRN 249

Query: 274 LANRESVILSLHPHNDRGTAVAAAELGFAAGADRIEGCLFGNGERTGNVCLVTLGLNLFS 333
           L+ RE + LS HPHNDRGT VA+AEL   AGADR+EGCLFG GERTGN+ +VT+G+NLFS
Sbjct: 250 LSRREFIALSSHPHNDRGTGVASAELAIMAGADRVEGCLFGQGERTGNLDIVTVGMNLFS 309

Query: 334 RGVDPQIDFSNIDEIRRTVEYCNQLPVHERHPYGGDLVYTAFSGSHQDAINKGLDAMKLD 393
           +GVDP +DFS+IDEIRR  EYCNQ+ V ERHPY GDLVYT+FSGSHQDAI KG +A++ D
Sbjct: 310 QGVDPMVDFSDIDEIRRVYEYCNQMTVPERHPYVGDLVYTSFSGSHQDAIKKGFEALEKD 369

Query: 394 ADAADCDVDDMLWQVPYLPIDPRDVGRTYEAVIRVNSQSGKGGVAYIMKTDHGLSLPRRL 453
           A+AA   V    W VPYLPIDP+DVGR+YEAVIRVNSQSGKGG++Y++K++H L LPRR+
Sbjct: 370 AEAAGVPVGQQTWGVPYLPIDPKDVGRSYEAVIRVNSQSGKGGISYVLKSEHQLDLPRRM 429

Query: 454 QIEFSQVIQKIAEGTAGEGGEVSPKEMWDAFAEEYLAPVRPLE------RIRQHVDAADD 507
           Q+EFS++IQ     T  EGGEV+P E+W  F +EYL    P E      R+R H  +   
Sbjct: 430 QVEFSKIIQ---TKTDTEGGEVTPAEIWSIFEDEYL----PTESAWGRIRLRSHQSSTTT 482

Query: 508 DGGTTSITATVKINGVETEISGSGNGPLAAFVHALADVGFDVAVLDYYEHAMSAGDDAQA 567
           DG    +   V ++G +T + G+GNGP+ AF  AL  VG DV +LDY EH  S G  AQA
Sbjct: 483 DGRDELVVDAV-VDGEDTVLKGAGNGPIDAFFDALGAVGVDVRLLDYVEHTRSQGAAAQA 541

Query: 568 AAYVEASVTIASPAQPGEAGRHASDPVTIASPAQPGEAGRHASDPVTSKTVWGVGIAPSI 627
           AAYVE +V        GE                              K VWGVG+  +I
Sbjct: 542 AAYVECAV--------GE------------------------------KVVWGVGVDNNI 563

Query: 628 TTASLRAVVSAVNRAAR 644
             ASL+A +SAVNRA +
Sbjct: 564 VRASLKAAISAVNRAEK 580


Lambda     K      H
   0.317    0.133    0.399 

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: 962
Number of extensions: 41
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 644
Length of database: 582
Length adjustment: 37
Effective length of query: 607
Effective length of database: 545
Effective search space:   330815
Effective search space used:   330815
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_037576554.1 BS73_RS26265 (2-isopropylmalate synthase)
to HMM TIGR00970 (leuA: 2-isopropylmalate synthase (EC 2.3.3.13))

# 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/TIGR00970.hmm
# target sequence database:        /tmp/gapView.1608477.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00970  [M=564]
Accession:   TIGR00970
Description: leuA_yeast: 2-isopropylmalate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-253  828.7   0.0   1.3e-253  828.5   0.0    1.0  1  NCBI__GCF_000744815.1:WP_037576554.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_037576554.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  828.5   0.0  1.3e-253  1.3e-253       1     563 [.      20     579 ..      20     580 .. 0.97

  Alignments for each domain:
  == domain 1  score: 828.5 bits;  conditional E-value: 1.3e-253
                             TIGR00970   1 pskkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkeievgfpsas 73 
                                           p ++ykpf ++ l++r+wp kvit+aprwls+dlrdGnqalidpms++rk+ +f+llvr+G+keievgfps+ 
  NCBI__GCF_000744815.1:WP_037576554.1  20 PFQRYKPFGTVDLPDRTWPGKVITKAPRWLSTDLRDGNQALIDPMSPARKRAMFDLLVRLGYKEIEVGFPSSG 92 
                                           779********************************************************************** PP

                             TIGR00970  74 qtdfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdlfrevvfrasreevlal 146
                                           qtdfdfvr iie+g+ip+dvti+vltq+re+li+rtve+l Ga++a+vh+ynat++lfr+vvfrasr+ev ++
  NCBI__GCF_000744815.1:WP_037576554.1  93 QTDFDFVRSIIEEGAIPEDVTISVLTQAREDLIERTVESLVGAPRATVHMYNATAPLFRRVVFRASRDEVRQI 165
                                           ************************************************************************* PP

                             TIGR00970 147 avegsklvrklvkdaaksketrwsfeyspesfsdtelefavevceavkeviepteerpiifnlpatvevatpn 219
                                           av+g+  v k +++ +  ++t ++++yspe f dtel+fa+evceav +v++p e r ii+nlp+tve +tpn
  NCBI__GCF_000744815.1:WP_037576554.1 166 AVDGTGHVMKYAEQLL-GEDTVFGYQYSPEIFVDTELDFALEVCEAVMDVWQPEEGREIILNLPTTVERCTPN 237
                                           **********999876.5789**************************************************** PP

                             TIGR00970 220 vyadsieylstniaerekvilslhphndrGtavaaaelGllaGadrieGclfGnGertGnvdlvtlalnlytq 292
                                           vyad+ie++s+n++ re + ls hphndrGt+va+ael ++aGadr+eGclfG+GertGn+d+vt+++nl++q
  NCBI__GCF_000744815.1:WP_037576554.1 238 VYADQIEWMSRNLSRREFIALSSHPHNDRGTGVASAELAIMAGADRVEGCLFGQGERTGNLDIVTVGMNLFSQ 310
                                           ************************************************************************* PP

                             TIGR00970 293 GvspnldfsdldeilrvvercnkipvherhpygGdlvvtafsGshqdaikkGldaldkkkaaa.....dtlwk 360
                                           Gv+p +dfsd+dei+rv e+cn++ v erhpy Gdlv+t+fsGshqdaikkG++al+k+++aa     ++ w 
  NCBI__GCF_000744815.1:WP_037576554.1 311 GVDPMVDFSDIDEIRRVYEYCNQMTVPERHPYVGDLVYTSFSGSHQDAIKKGFEALEKDAEAAgvpvgQQTWG 383
                                           ***********************************************************99988999999*** PP

                             TIGR00970 361 vpylpldpkdvgreyeavirvnsqsGkGGvayvlktdlGldlprrlqiefssvvkdiadskGkelsskeisdl 433
                                           vpylp+dpkdvgr yeavirvnsqsGkGG++yvlk ++ ldlprr+q+efs++++  +d++G+e+++ ei+ +
  NCBI__GCF_000744815.1:WP_037576554.1 384 VPYLPIDPKDVGRSYEAVIRVNSQSGKGGISYVLKSEHQLDLPRRMQVEFSKIIQTKTDTEGGEVTPAEIWSI 456
                                           ************************************************************************* PP

                             TIGR00970 434 fkeeyllnveqlerislvdyaveddGteskvitavvkikgekkdieGsGnGplsalvdaladllnvdvavady 506
                                           f++eyl ++   +ri+l++++ + +  ++  +     ++ge + ++G+GnGp+ a+ dal  ++ vdv ++dy
  NCBI__GCF_000744815.1:WP_037576554.1 457 FEDEYLPTESAWGRIRLRSHQSSTTTDGRDELVVDAVVDGEDTVLKGAGNGPIDAFFDALGAVG-VDVRLLDY 528
                                           *************9998777666555555555555556789999******************99.******** PP

                             TIGR00970 507 sehalgsGddakaasyvelsvrrasdaekatvwGvGiaedvtsaslravlsavnraa 563
                                            eh+ + G  a+aa+yve +v ++       vwGvG+++++  asl+a +savnra 
  NCBI__GCF_000744815.1:WP_037576554.1 529 VEHTRSQGAAAQAAAYVECAVGEKV------VWGVGVDNNIVRASLKAAISAVNRAE 579
                                           *******************998877......************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (564 nodes)
Target sequences:                          1  (582 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: 00:00:00.01
# Mc/sec: 23.67
//
[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