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

GapMind for Amino acid biosynthesis

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

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

Query= SwissProt::P42455
         (616 letters)



>FitnessBrowser__Burk376:H281DRAFT_00385
          Length = 572

 Score =  604 bits (1558), Expect = e-177
 Identities = 319/571 (55%), Positives = 397/571 (69%), Gaps = 33/571 (5%)

Query: 37  PVNRYMPFEVEVEDISLPDRTWPDKKITVAPQWCAVDLRDGNQALIDPMSPERKRRMFEL 96
           P  +Y  F+     I+L DR WP + IT AP W + DLRDGNQAL +PM+ ERK RMF+ 
Sbjct: 5   PATKYRSFK----PINLTDRQWPSRTITRAPIWMSTDLRDGNQALFEPMNAERKMRMFKT 60

Query: 97  LVQMGFKEIEVGFPSASQTDFDFVREIIEKGMIPDDVTIQVLVQAREHLIRRTFEACEGA 156
           LVQ+GFKEIEV FPSASQTDF+FVRE+IE G IPDDVTI+VL QAR+ LI RTFE+  GA
Sbjct: 61  LVQIGFKEIEVAFPSASQTDFNFVRELIEGGHIPDDVTIEVLTQARDDLIERTFESLRGA 120

Query: 157 KNVIVHFYNSTSILQRNVVFRMDKVQVKKLATDAAELIKTIAQDYPDTNWRWQYSPESFT 216
              IVH YN+T+   R +VF +D+  VK+LA  AA  +K +A   P+T++  QYSPE F+
Sbjct: 121 PRAIVHLYNATAPEFRKIVFGLDQNGVKELAQKAARTMKRLADAAPETHFTLQYSPEVFS 180

Query: 217 GTEVEYAKEVVDAVVEVMDPTPENPMIINLPSTVEMITPNVYADSIEWMHRNLNRRDSII 276
           GTE+E+AKEV DAV ++  PTPE+  I+NLP+TVEM TPNVYAD IEWMHRNL RRDS+I
Sbjct: 181 GTELEFAKEVCDAVFDIWQPTPEHKAIVNLPATVEMATPNVYADQIEWMHRNLARRDSLI 240

Query: 277 LSLHPHNDRGTGVGAAELGYMAGADRIEGCLFGNGERTGNVCLVTLALNMLTQGVDPQLD 336
           +S+HPHNDRGT V AAEL  MAGADRIEGCLFGNGERTGNV LVTLALN+ TQGVDP LD
Sbjct: 241 VSVHPHNDRGTAVAAAELAVMAGADRIEGCLFGNGERTGNVDLVTLALNLYTQGVDPGLD 300

Query: 337 FTDIRQIRSTVEYCNQLRVPERHPYGGDLVFTAFSGSHQDAVNKGLDAMAAKVQPGASST 396
           F++I +I  T E C QL V  RHPY GDLVFTAFSGSHQDA+ KG               
Sbjct: 301 FSNINEIARTAEECTQLPVHPRHPYVGDLVFTAFSGSHQDAIKKGFAV------------ 348

Query: 397 EVSWEQLRDTEWEVPYLPIDPKDVGRDYEAVIRVNSQSGKGGVAYIMKTDHGLQIPRSMQ 456
                Q  D  WEVPY+PIDP D+GR Y++VIRVNSQSGKGG+AY+++  +G+ +PR +Q
Sbjct: 349 -----QKPDAMWEVPYMPIDPNDLGRTYDSVIRVNSQSGKGGIAYLLEQSYGVVLPRRLQ 403

Query: 457 VEFSTVVQNVTDAEGGEVNSKAMWDIFATEYLERTAPVEQIALRVENAQTENEDASITAE 516
           V+FS+ VQ  TD  G EV    +W++F  EY++  APV  I   + + Q   E   +T +
Sbjct: 404 VDFSSAVQRFTDDSGQEVTPSQIWELFQQEYVQNIAPVHYIGHSL-SEQDGRERIKLTVD 462

Query: 517 LIHNGKDVTVDGRGNGPLAAYANALEKLGIDVEIQEYNQHARTSGDDAEAAAYVLAEVNG 576
           +  NG    ++G GNGPL A  +A   +G+ V IQ Y + A T G DA A A  +AE+ G
Sbjct: 463 I--NGTRRVLNGEGNGPLDALMHA---MGVPVRIQHYEERALTQGADARAVA--VAEMAG 515

Query: 577 RKV----WGVGIAGSITYASLKAVTSAVNRA 603
             V    +GVGI  ++  AS++AV S VNRA
Sbjct: 516 ADVTGSAFGVGIDANLVTASIRAVISGVNRA 546


Lambda     K      H
   0.316    0.133    0.390 

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: 940
Number of extensions: 39
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: 616
Length of database: 572
Length adjustment: 37
Effective length of query: 579
Effective length of database: 535
Effective search space:   309765
Effective search space used:   309765
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 (21.6 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.23914.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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 7.54
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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:

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
the source code
instructions for running GapMind on your computer
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