GapMind for Amino acid biosynthesis

 

Aligments for a candidate for leuA in Pseudomonas fluorescens FW300-N1B4

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate Pf1N1B4_847 2-isopropylmalate synthase (EC 2.3.3.13)

Query= BRENDA::P9WQB3
         (644 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_847 2-isopropylmalate
           synthase (EC 2.3.3.13)
          Length = 559

 Score =  579 bits (1492), Expect = e-169
 Identities = 310/604 (51%), Positives = 404/604 (66%), Gaps = 63/604 (10%)

Query: 42  PVNRYRPFAEEVEPIRLRNRTWPDRVIDRAPLWCAVDLRDGNQALIDPMSPARKRRMFDL 101
           P ++YR F      I + +RTWP + I  AP+WC+ DLRDGNQ+LI+PM   +K R +  
Sbjct: 7   PSSKYRAFPT----IDIPDRTWPSKTITAAPIWCSSDLRDGNQSLIEPMDAVKKLRFWKT 62

Query: 102 LVRMGYKEIEVGFPSASQTDFDFVREIIEQGAIPDDVTIQVLTQCRPELIERTFQACSGA 161
           LV++G KEIE  FP+ASQTDFDFVR +IE G IPDD TIQVLTQ R +LI RTF++  GA
Sbjct: 63  LVQVGVKEIEASFPAASQTDFDFVRTLIEDGHIPDDTTIQVLTQGREDLIARTFESLRGA 122

Query: 162 PRAIVHFYNSTSILQRRVVFRANRAEVQAIATDGARKCVEQAAKYPGTQWRFEYSPESYT 221
            +AIVH YN+TS   RR+VF  ++  ++AIA + A+  V+ AA+ P T+W FEYSPE+++
Sbjct: 123 KKAIVHLYNATSPSFRRIVFNQDKDGIKAIAVNAAKLFVKYAAQQPDTEWTFEYSPETFS 182

Query: 222 GTELEYAKQVCDAVGEVIAPTPERPIIFNLPATVEMTTPNVYADSIEWMSRNLANRESVI 281
            TELE+AK+VCDAV EV  PTPE  +I NLPATVE  TPN+YAD IEW  R++  R+SVI
Sbjct: 183 ATELEFAKEVCDAVIEVWNPTPEHKVILNLPATVECATPNIYADQIEWFGRHINRRDSVI 242

Query: 282 LSLHPHNDRGTAVAAAELGFAAGADRIEGCLFGNGERTGNVCLVTLGLNLFSRGVDPQID 341
           +SLH HNDRGT VAA ELG  AGADR+EGCLFGNGERTGNV LVT+ LNL+++GVDP++D
Sbjct: 243 ISLHTHNDRGTGVAATELGLMAGADRVEGCLFGNGERTGNVDLVTVALNLYTQGVDPELD 302

Query: 342 FSNIDEIRRTVEYCNQLPVHERHPYGGDLVYTAFSGSHQDAINKGLDAMKLDADAADCDV 401
           FS+ID +R+ VE CNQ+ VH RHPY GDLV+TAFSGSHQDAI KG    + DA       
Sbjct: 303 FSDIDGVRKVVEECNQIQVHPRHPYVGDLVHTAFSGSHQDAIRKGFAQQQPDA------- 355

Query: 402 DDMLWQVPYLPIDPRDVGRTYEAVIRVNSQSGKGGVAYIMKTDHGLSLPRRLQIEFSQVI 461
              LW+VPYLPIDP D+GR+YEAVIRVNSQSGKGG+AY+++ ++G++LPRR+QIEFSQV+
Sbjct: 356 ---LWEVPYLPIDPADIGRSYEAVIRVNSQSGKGGIAYLLEQEYGINLPRRMQIEFSQVV 412

Query: 462 QKIAEGTAGEGGEVSPKEMWDAFAEEYLAPVRPLERIRQHVDAADDDGGTTSITATVKIN 521
           Q+    T   G E++ +++      EYL    P   +   +    ++ G +++   V   
Sbjct: 413 QR---ETDRLGLEMTAQQIHALLHSEYLQANTPYALVSHRL---QEENGHSAVEVEVSSK 466

Query: 522 GV-ETEI--SGSGNGPLAAFVHALADVGFDVAVLDYYEHAMSAGDDAQAAAYVEASVTIA 578
           G  ET +   G GNG L A V   A +   V ++DY EHA+ AG +A+AAAY+E  V   
Sbjct: 467 GQGETNLHWRGKGNGALEALV---AGLPIPVEIMDYNEHAIGAGTNAKAAAYIELRVN-- 521

Query: 579 SPAQPGEAGRHASDPVTIASPAQPGEAGRHASDPVTSKTVWGVGIAPSITTASLRAVVSA 638
                GE                              + V GVGI  +ITTAS +A+ SA
Sbjct: 522 -----GE------------------------------RAVHGVGIDENITTASFKALFSA 546

Query: 639 VNRA 642
           +NR+
Sbjct: 547 LNRS 550


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: 915
Number of extensions: 42
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 644
Length of database: 559
Length adjustment: 37
Effective length of query: 607
Effective length of database: 522
Effective search space:   316854
Effective search space used:   316854
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 Pf1N1B4_847 (2-isopropylmalate synthase (EC 2.3.3.13))
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.19036.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
     1e-242  792.6   0.0   1.2e-242  792.4   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_847  2-isopropylmalate synthase (EC 2


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_847  2-isopropylmalate synthase (EC 2.3.3.13)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  792.4   0.0  1.2e-242  1.2e-242       1     562 [.       7     550 ..       7     552 .. 0.95

  Alignments for each domain:
  == domain 1  score: 792.4 bits;  conditional E-value: 1.2e-242
                                     TIGR00970   1 pskkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkei 65 
                                                   ps+ky+ f +i +++r+wp k it ap w+s dlrdGnq+li+pm++ +k r++k lv++G kei
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_847   7 PSSKYRAFPTIDIPDRTWPSKTITAAPIWCSSDLRDGNQSLIEPMDAVKKLRFWKTLVQVGVKEI 71 
                                                   99*************************************************************** PP

                                     TIGR00970  66 evgfpsasqtdfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdl 130
                                                   e +fp+asqtdfdfvr +ie+g ipdd tiqvltq re+li rt+e+l+Gakkaivhlynats+ 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_847  72 EASFPAASQTDFDFVRTLIEDGHIPDDTTIQVLTQGREDLIARTFESLRGAKKAIVHLYNATSPS 136
                                                   ***************************************************************** PP

                                     TIGR00970 131 frevvfrasreevlalavegsklvrklvkdaaksketrwsfeyspesfsdtelefavevceavke 195
                                                   fr++vf+++++ + a+av+++kl    vk aa++++t+w+feyspe+fs telefa+evc+av e
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_847 137 FRRIVFNQDKDGIKAIAVNAAKL---FVKYAAQQPDTEWTFEYSPETFSATELEFAKEVCDAVIE 198
                                                   ********************665...6889999******************************** PP

                                     TIGR00970 196 viepteerpiifnlpatvevatpnvyadsieylstniaerekvilslhphndrGtavaaaelGll 260
                                                   v++pt+e+ +i+nlpatve atpn+yad+ie++ ++i  r++vi+slh+hndrGt+vaa+elGl+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_847 199 VWNPTPEHKVILNLPATVECATPNIYADQIEWFGRHINRRDSVIISLHTHNDRGTGVAATELGLM 263
                                                   ***************************************************************** PP

                                     TIGR00970 261 aGadrieGclfGnGertGnvdlvtlalnlytqGvspnldfsdldeilrvvercnkipvherhpyg 325
                                                   aGadr+eGclfGnGertGnvdlvt+alnlytqGv+p+ldfsd+d +++vve+cn+i+vh+rhpy 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_847 264 AGADRVEGCLFGNGERTGNVDLVTVALNLYTQGVDPELDFSDIDGVRKVVEECNQIQVHPRHPYV 328
                                                   ***************************************************************** PP

                                     TIGR00970 326 GdlvvtafsGshqdaikkGldaldkkkaaadtlwkvpylpldpkdvgreyeavirvnsqsGkGGv 390
                                                   Gdlv+tafsGshqdai+kG+  +     + d+lw+vpylp+dp d+gr yeavirvnsqsGkGG+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_847 329 GDLVHTAFSGSHQDAIRKGFAQQ-----QPDALWEVPYLPIDPADIGRSYEAVIRVNSQSGKGGI 388
                                                   ********************754.....45789******************************** PP

                                     TIGR00970 391 ayvlktdlGldlprrlqiefssvvkdiadskGkelsskeisdlfkeeyllnveqlerislvdyav 455
                                                   ay+l +++G++lprr+qiefs+vv+  +d  G e+++++i  l++ eyl ++ ++  +s +    
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_847 389 AYLLEQEYGINLPRRMQIEFSQVVQRETDRLGLEMTAQQIHALLHSEYLQANTPYALVSHRL--Q 451
                                                   **************************************************888887776543..4 PP

                                     TIGR00970 456 eddGteskvitavvkikgekkd...ieGsGnGplsalvdaladllnvdvavadysehalgsGdda 517
                                                   e++G    +++  v  kg+        G GnG l alv  l     + v+++dy+eha+g+G +a
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_847 452 EENGH--SAVEVEVSSKGQGETnlhWRGKGNGALEALVAGLP----IPVEIMDYNEHAIGAGTNA 510
                                                   67774..45555555555432223489*********998874....788**************** PP

                                     TIGR00970 518 kaasyvelsvrrasdaekatvwGvGiaedvtsaslravlsavnra 562
                                                   kaa+y+el v+ +       v GvGi+e++t+as++a++sa+nr 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_847 511 KAAAYIELRVNGER-----AVHGVGIDENITTASFKALFSALNRS 550
                                                   ********998766.....799*********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (564 nodes)
Target sequences:                          1  (559 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: 00:00:00.02
# Mc/sec: 11.91
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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