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.1384959.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 31.57
//
[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:

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