Aligments for a candidate for leuA in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Aligments for a candidate for leuA in Paraburkholderia bryophila 376MFSha3.1

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate H281DRAFT_00385 H281DRAFT_00385 2-isopropylmalate synthase

Query= BRENDA::P9WQB3
         (644 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_00385 H281DRAFT_00385
           2-isopropylmalate synthase
          Length = 572

 Score =  611 bits (1576), Expect = e-179
 Identities = 323/601 (53%), Positives = 404/601 (67%), Gaps = 59/601 (9%)

Query: 42  PVNRYRPFAEEVEPIRLRNRTWPDRVIDRAPLWCAVDLRDGNQALIDPMSPARKRRMFDL 101
           P  +YR F    +PI L +R WP R I RAP+W + DLRDGNQAL +PM+  RK RMF  
Sbjct: 5   PATKYRSF----KPINLTDRQWPSRTITRAPIWMSTDLRDGNQALFEPMNAERKMRMFKT 60

Query: 102 LVRMGYKEIEVGFPSASQTDFDFVREIIEQGAIPDDVTIQVLTQCRPELIERTFQACSGA 161
           LV++G+KEIEV FPSASQTDF+FVRE+IE G IPDDVTI+VLTQ R +LIERTF++  GA
Sbjct: 61  LVQIGFKEIEVAFPSASQTDFNFVRELIEGGHIPDDVTIEVLTQARDDLIERTFESLRGA 120

Query: 162 PRAIVHFYNSTSILQRRVVFRANRAEVQAIATDGARKCVEQAAKYPGTQWRFEYSPESYT 221
           PRAIVH YN+T+   R++VF  ++  V+ +A   AR     A   P T +  +YSPE ++
Sbjct: 121 PRAIVHLYNATAPEFRKIVFGLDQNGVKELAQKAARTMKRLADAAPETHFTLQYSPEVFS 180

Query: 222 GTELEYAKQVCDAVGEVIAPTPERPIIFNLPATVEMTTPNVYADSIEWMSRNLANRESVI 281
           GTELE+AK+VCDAV ++  PTPE   I NLPATVEM TPNVYAD IEWM RNLA R+S+I
Sbjct: 181 GTELEFAKEVCDAVFDIWQPTPEHKAIVNLPATVEMATPNVYADQIEWMHRNLARRDSLI 240

Query: 282 LSLHPHNDRGTAVAAAELGFAAGADRIEGCLFGNGERTGNVCLVTLGLNLFSRGVDPQID 341
           +S+HPHNDRGTAVAAAEL   AGADRIEGCLFGNGERTGNV LVTL LNL+++GVDP +D
Sbjct: 241 VSVHPHNDRGTAVAAAELAVMAGADRIEGCLFGNGERTGNVDLVTLALNLYTQGVDPGLD 300

Query: 342 FSNIDEIRRTVEYCNQLPVHERHPYGGDLVYTAFSGSHQDAINKGLDAMKLDADAADCDV 401
           FSNI+EI RT E C QLPVH RHPY GDLV+TAFSGSHQDAI KG    K DA       
Sbjct: 301 FSNINEIARTAEECTQLPVHPRHPYVGDLVFTAFSGSHQDAIKKGFAVQKPDA------- 353

Query: 402 DDMLWQVPYLPIDPRDVGRTYEAVIRVNSQSGKGGVAYIMKTDHGLSLPRRLQIEFSQVI 461
              +W+VPY+PIDP D+GRTY++VIRVNSQSGKGG+AY+++  +G+ LPRRLQ++FS  +
Sbjct: 354 ---MWEVPYMPIDPNDLGRTYDSVIRVNSQSGKGGIAYLLEQSYGVVLPRRLQVDFSSAV 410

Query: 462 QKIAEGTAGEGGEVSPKEMWDAFAEEYLAPVRPLERIRQHVDAADDDGGTTSITATVKIN 521
           Q+    T   G EV+P ++W+ F +EY+  + P+  I   +   D   G   I  TV IN
Sbjct: 411 QRF---TDDSGQEVTPSQIWELFQQEYVQNIAPVHYIGHSLSEQD---GRERIKLTVDIN 464

Query: 522 GVETEISGSGNGPLAAFVHALADVGFDVAVLDYYEHAMSAGDDAQAAAYVEASVTIASPA 581
           G    ++G GNGPL A +HA+   G  V +  Y E A++ G DA+A A  E         
Sbjct: 465 GTRRVLNGEGNGPLDALMHAM---GVPVRIQHYEERALTQGADARAVAVAEM-------- 513

Query: 582 QPGEAGRHASDPVTIASPAQPGEAGRHASDPVTSKTVWGVGIAPSITTASLRAVVSAVNR 641
                                      A   VT  + +GVGI  ++ TAS+RAV+S VNR
Sbjct: 514 ---------------------------AGADVTG-SAFGVGIDANLVTASIRAVISGVNR 545

Query: 642 A 642
           A
Sbjct: 546 A 546


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: 904
Number of extensions: 31
Number of successful extensions: 4
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: 644
Length of database: 572
Length adjustment: 37
Effective length of query: 607
Effective length of database: 535
Effective search space:   324745
Effective search space used:   324745
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 H281DRAFT_00385 H281DRAFT_00385 (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.24522.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   4.2e-240  784.0   0.0     5e-240  783.7   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_00385  H281DRAFT_00385 2-isopropylmalat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_00385  H281DRAFT_00385 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  783.7   0.0    5e-240    5e-240       1     562 [.       5     546 ..       5     548 .. 0.96

  Alignments for each domain:
  == domain 1  score: 783.7 bits;  conditional E-value: 5e-240
                                    TIGR00970   1 pskkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkeie 66 
                                                  p+ ky+ fk+i+l++r+wp + itrap w+s+dlrdGnqal +pm++erk r+fk lv+iGfkeie
  lcl|FitnessBrowser__Burk376:H281DRAFT_00385   5 PATKYRSFKPINLTDRQWPSRTITRAPIWMSTDLRDGNQALFEPMNAERKMRMFKTLVQIGFKEIE 70 
                                                  889*************************************************************** PP

                                    TIGR00970  67 vgfpsasqtdfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdlfr 132
                                                  v+fpsasqtdf+fvre+ie g ipddvti+vltq+r++li+rt+e+l+Ga++aivhlynat++ fr
  lcl|FitnessBrowser__Burk376:H281DRAFT_00385  71 VAFPSASQTDFNFVRELIEGGHIPDDVTIEVLTQARDDLIERTFESLRGAPRAIVHLYNATAPEFR 136
                                                  ****************************************************************** PP

                                    TIGR00970 133 evvfrasreevlalavegsklvrklvkdaaksketrwsfeyspesfsdtelefavevceavkevie 198
                                                  ++vf  +++ v +la +++   r + + a   +et+++ +yspe fs+telefa+evc+av ++++
  lcl|FitnessBrowser__Burk376:H281DRAFT_00385 137 KIVFGLDQNGVKELAQKAA---RTMKRLADAAPETHFTLQYSPEVFSGTELEFAKEVCDAVFDIWQ 199
                                                  *****************95...5555556667899******************************* PP

                                    TIGR00970 199 pteerpiifnlpatvevatpnvyadsieylstniaerekvilslhphndrGtavaaaelGllaGad 264
                                                  pt+e+  i nlpatve+atpnvyad+ie++ +n+a r+++i+s+hphndrGtavaaael ++aGad
  lcl|FitnessBrowser__Burk376:H281DRAFT_00385 200 PTPEHKAIVNLPATVEMATPNVYADQIEWMHRNLARRDSLIVSVHPHNDRGTAVAAAELAVMAGAD 265
                                                  ****************************************************************** PP

                                    TIGR00970 265 rieGclfGnGertGnvdlvtlalnlytqGvspnldfsdldeilrvvercnkipvherhpygGdlvv 330
                                                  rieGclfGnGertGnvdlvtlalnlytqGv+p ldfs+++ei r+ e+c ++pvh+rhpy Gdlv+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00385 266 RIEGCLFGNGERTGNVDLVTLALNLYTQGVDPGLDFSNINEIARTAEECTQLPVHPRHPYVGDLVF 331
                                                  ****************************************************************** PP

                                    TIGR00970 331 tafsGshqdaikkGldaldkkkaaadtlwkvpylpldpkdvgreyeavirvnsqsGkGGvayvlkt 396
                                                  tafsGshqdaikkG+ +++      d++w+vpy+p+dp+d+gr+y++virvnsqsGkGG+ay+l +
  lcl|FitnessBrowser__Burk376:H281DRAFT_00385 332 TAFSGSHQDAIKKGFAVQKP-----DAMWEVPYMPIDPNDLGRTYDSVIRVNSQSGKGGIAYLLEQ 392
                                                  ***************99864.....669************************************** PP

                                    TIGR00970 397 dlGldlprrlqiefssvvkdiadskGkelsskeisdlfkeeyllnveqlerislvdyaveddGtes 462
                                                  ++G+ lprrlq++fss+v+ ++d  G+e+++++i++lf++ey  n  +++ i       e+dG  +
  lcl|FitnessBrowser__Burk376:H281DRAFT_00385 393 SYGVVLPRRLQVDFSSAVQRFTDDSGQEVTPSQIWELFQQEYVQNIAPVHYIGHS--LSEQDG--R 454
                                                  ********************************************99999888654..446677..7 PP

                                    TIGR00970 463 kvitavvkikgekkdieGsGnGplsalvdaladllnvdvavadysehalgsGddakaasyvelsvr 528
                                                  + i+ +v+i+g+++ ++G GnGpl al++a+     v v + +y e al+ G da+a +  e++  
  lcl|FitnessBrowser__Burk376:H281DRAFT_00385 455 ERIKLTVDINGTRRVLNGEGNGPLDALMHAMG----VPVRIQHYEERALTQGADARAVAVAEMAGA 516
                                                  889*********************99999974....7789*****************998887655 PP

                                    TIGR00970 529 rasdaekatvwGvGiaedvtsaslravlsavnra 562
                                                         +  +GvGi++++ +as+rav+s+vnra
  lcl|FitnessBrowser__Burk376:H281DRAFT_00385 517 DV----TGSAFGVGIDANLVTASIRAVISGVNRA 546
                                                  44....5899**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (564 nodes)
Target sequences:                          1  (572 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 10.72
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for Amino acid biosynthesis