GapMind for Amino acid biosynthesis

 

Aligments for a candidate for leuA in Pseudomonas fluorescens GW456-L13

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate PfGW456L13_4854 2-isopropylmalate synthase (EC 2.3.3.13)

Query= BRENDA::P9WQB3
         (644 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854
           2-isopropylmalate synthase (EC 2.3.3.13)
          Length = 559

 Score =  576 bits (1485), Expect = e-169
 Identities = 311/604 (51%), Positives = 403/604 (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   IPDD TIQVLTQ R +LIERTF++  GA
Sbjct: 63  LVQVGVKEIEASFPAASQTDFDFVRTLIEGNHIPDDTTIQVLTQGREDLIERTFESLRGA 122

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

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

Query: 282 LSLHPHNDRGTAVAAAELGFAAGADRIEGCLFGNGERTGNVCLVTLGLNLFSRGVDPQID 341
           +SLH HNDRGT VAA ELG  AGADR+EGCLFGNGERTGNV LVT+ LNL+++GV+P++D
Sbjct: 243 ISLHTHNDRGTGVAATELGLMAGADRVEGCLFGNGERTGNVDLVTVALNLYTQGVNPELD 302

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

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

Query: 462 QKIAEGTAGEGGEVSPKEMWDAFAEEYLAPVRPLERIRQHVDAADDDGGTTSITATVKIN 521
           Q+    T   G E++ +++      EYL    P   +   +    ++ G +++   V   
Sbjct: 413 QR---ETDRLGLEMTAQQIHALLHSEYLQANTPYALVSHRL---QEENGHSAVEVEVASQ 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---AGLPVPVEIMDYNEHAIGAGTNAKAAAYIELRVN-- 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: 925
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 PfGW456L13_4854 (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.323.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-241  789.1   0.0   1.4e-241  788.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854  2-isopropylmalate synthase (EC 2


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854  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 !  788.8   0.0  1.4e-241  1.4e-241       1     562 [.       7     550 ..       7     552 .. 0.95

  Alignments for each domain:
  == domain 1  score: 788.8 bits;  conditional E-value: 1.4e-241
                                               TIGR00970   1 pskkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfk 55 
                                                             ps+ky+ f +i +++r+wp k it ap w+s dlrdGnq+li+pm++ +k r++k
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854   7 PSSKYRAFPTIDIPDRTWPSKTITAAPIWCSSDLRDGNQSLIEPMDAVKKLRFWK 61 
                                                             99***************************************************** PP

                                               TIGR00970  56 llvriGfkeievgfpsasqtdfdfvreiieqglipddvtiqvltqsreelikrtv 110
                                                              lv++G keie +fp+asqtdfdfvr +ie + ipdd tiqvltq re+li+rt+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854  62 TLVQVGVKEIEASFPAASQTDFDFVRTLIEGNHIPDDTTIQVLTQGREDLIERTF 116
                                                             ******************************************************* PP

                                               TIGR00970 111 ealsGakkaivhlynatsdlfrevvfrasreevlalavegsklvrklvkdaaksk 165
                                                             e+l+Gakkaivhlynats+ fr++vf+++++ v a+av+++kl    vk aa ++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854 117 ESLRGAKKAIVHLYNATSPSFRRIVFNQDKDGVKAIAVNAAKL---FVKYAAMQP 168
                                                             ****************************************665...78899**** PP

                                               TIGR00970 166 etrwsfeyspesfsdtelefavevceavkeviepteerpiifnlpatvevatpnv 220
                                                             +t+w+feyspe+fs te+efa+evc+av ev++pt+e+ +i+nlpatve atpn+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854 169 DTEWTFEYSPETFSATEMEFAKEVCDAVIEVWNPTPEHKMILNLPATVECATPNI 223
                                                             ******************************************************* PP

                                               TIGR00970 221 yadsieylstniaerekvilslhphndrGtavaaaelGllaGadrieGclfGnGe 275
                                                             yad+ie++ ++i  r++vi+slh+hndrGt+vaa+elGl+aGadr+eGclfGnGe
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854 224 YADQIEWFGRHINRRDSVIISLHTHNDRGTGVAATELGLMAGADRVEGCLFGNGE 278
                                                             ******************************************************* PP

                                               TIGR00970 276 rtGnvdlvtlalnlytqGvspnldfsdldeilrvvercnkipvherhpygGdlvv 330
                                                             rtGnvdlvt+alnlytqGv+p+ldfsd+d +++vve+cn+i+vh+rhpy Gdlv+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854 279 RTGNVDLVTVALNLYTQGVNPELDFSDIDGVRKVVEECNQIQVHPRHPYVGDLVH 333
                                                             ******************************************************* PP

                                               TIGR00970 331 tafsGshqdaikkGldaldkkkaaadtlwkvpylpldpkdvgreyeavirvnsqs 385
                                                             tafsGshqdai+kG+  ++      d+lw+vpylp+dp d+gr yeavirvnsqs
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854 334 TAFSGSHQDAIRKGFAQQK-----PDALWEVPYLPIDPADIGRSYEAVIRVNSQS 383
                                                             ***************7654.....4679*************************** PP

                                               TIGR00970 386 GkGGvayvlktdlGldlprrlqiefssvvkdiadskGkelsskeisdlfkeeyll 440
                                                             GkGG+ay+l +++G++lprr+qiefs+vv+  +d  G e+++++i  l++ eyl 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854 384 GKGGIAYLLEQEYGISLPRRMQIEFSQVVQRETDRLGLEMTAQQIHALLHSEYLQ 438
                                                             ******************************************************* PP

                                               TIGR00970 441 nveqlerislvdyaveddGteskvitavvkikge...kkdieGsGnGplsalvda 492
                                                             ++ ++  +s +    e++G  + +++  v  +g+   + +  G GnG l alv  
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854 439 ANTPYALVSHRL--QEENG--HSAVEVEVASQGQgetNLHWRGKGNGALEALVAG 489
                                                             888887776554..46677..344444454444410134589*********9998 PP

                                               TIGR00970 493 ladllnvdvavadysehalgsGddakaasyvelsvrrasdaekatvwGvGiaedv 547
                                                             l     v v+++dy+eha+g+G +akaa+y+el v+ +       v GvGi+e++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854 490 LP----VPVEIMDYNEHAIGAGTNAKAAAYIELRVNGER-----AVHGVGIDENI 535
                                                             75....778************************998766.....799******** PP

                                               TIGR00970 548 tsaslravlsavnra 562
                                                             t+as++a++sa+nr 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854 536 TTASFKALFSALNRS 550
                                                             *************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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.89
//
[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 preprint 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