GapMind for Amino acid biosynthesis

 

Aligments for a candidate for leuA in Sphingomonas koreensis DSMZ 15582

Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate Ga0059261_4031 Ga0059261_4031 2-isopropylmalate synthase, yeast type

Query= SwissProt::P06208
         (619 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_4031 Ga0059261_4031
           2-isopropylmalate synthase, yeast type
          Length = 554

 Score =  567 bits (1461), Expect = e-166
 Identities = 295/561 (52%), Positives = 366/561 (65%), Gaps = 15/561 (2%)

Query: 31  MLKDPSSKYKPFNAPKLSNRKWPDNRITRAPRWLSTDLRDGNQSLPDPMSVEQKKEYFHK 90
           ML+DPS KY+PF    L +R+WP+  ITRAPRWLSTD+RDGNQ+L DPM  E+K  +F  
Sbjct: 1   MLRDPSVKYRPFPPIALPDRQWPNRTITRAPRWLSTDMRDGNQALIDPMDAEKKTRFFDL 60

Query: 91  LVNIGFKEIEVSFPSASQTDFDFTRYAVEN--APDDVSIQCLVQSREHLIKRTVEALTGA 148
           +  +G KEIEV FPSA  T+FDF    V +   PDDV++Q L Q+R  LI  T E+L GA
Sbjct: 61  ICRVGIKEIEVGFPSAGATEFDFISGLVRDNRIPDDVTVQVLTQARRDLIDTTFESLRGA 120

Query: 149 KKATIHTYLATSDMFREIVFNMSREEAISKAVEATKLVRKLTKDDPSQQATRWSYEFSPE 208
           K   +H Y A S  +R+IVF M R E    A++A KL+R      P    T W +++SPE
Sbjct: 121 KTGIVHVYNAVSPAWRKIVFGMDRAEVKQIAIDAAKLLRDNAAAQPD---TDWHFQYSPE 177

Query: 209 CFSDTPGEFAVEICEAVKKAWEPTEENPIIFNLPATVEVASPNVYADQIEYFATHITERE 268
            FS    +F+VE+C AV    +PT E PIIFNLPATVE A+PN+YADQIEYF  +I  R+
Sbjct: 178 TFSTAEIDFSVEVCAAVMDVLQPTVERPIIFNLPATVECATPNIYADQIEYFCRNIPNRD 237

Query: 269 KVCISTHCHNDRGCGVAATELGMLAGADRVEGCLFGNGERTGNVDLVTVAMNMYTQGVSP 328
            V +S H HNDRG GVAA ELGM+AGADRVEGCL GNGERTGN DLVTVAMNMYTQGV P
Sbjct: 238 AVVVSLHTHNDRGTGVAAAELGMMAGADRVEGCLLGNGERTGNCDLVTVAMNMYTQGVDP 297

Query: 329 NLDFSDLTSVLDVVERCNKIPVSQRAPYGGDLVVCAFSGSHQDAIKKGFNLQNKKRAQGE 388
            LDFSD+  ++  VE C  IPV  R PY GDLV  AFSGSHQDAIKKGF  Q    A+ +
Sbjct: 298 GLDFSDIDEIVKTVEYCTNIPVHPRTPYAGDLVFTAFSGSHQDAIKKGFAAQ---EARND 354

Query: 389 TQWRIPYLPLDPKDIGRDYEAVIRVNSQSGKGGAAWVILRSLGLDLPRNMQIEFSSAVQD 448
             W +PYLP+DP D+GR YEAVIRVNSQSGKGG AWV+ +  GL LP+ +Q +FS  VQ 
Sbjct: 355 QYWEVPYLPIDPADLGRSYEAVIRVNSQSGKGGVAWVLEQDKGLKLPKRLQADFSRHVQR 414

Query: 449 HADSLGRELKSDEISKLFKEAYNYNDEQYQAISLVNYNVEKFGTERRVFTGQVKVGDQIV 508
            AD   REL + +I   F E Y    +  Q  +L  Y+  +     R+F G ++V     
Sbjct: 415 VADESSRELNAQDIWATFVETYRL--KHPQRFTLGAYDETRASNGERIFAGSIEVDGVQQ 472

Query: 509 DIEGTGNGPISSLVDALSNLLNVRFAVANYTEHSLGSGSSTQAASYIHLSYRRNADNEKA 568
            + G GNG ISS+V A+     V   +A+Y EH++G GS  QAA+Y+     R AD    
Sbjct: 473 SVSGRGNGLISSVVAAMREGFGVDLDIADYAEHAIGHGSGAQAAAYVEC---RTADGRTV 529

Query: 569 YKWGVGVSEDVGDSSVRAIFA 589
             WGVG+ EDV  +SVRA+ +
Sbjct: 530 --WGVGIDEDVATASVRAVLS 548


Lambda     K      H
   0.315    0.131    0.379 

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: 819
Number of extensions: 35
Number of successful extensions: 6
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: 619
Length of database: 554
Length adjustment: 37
Effective length of query: 582
Effective length of database: 517
Effective search space:   300894
Effective search space used:   300894
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 Ga0059261_4031 Ga0059261_4031 (2-isopropylmalate synthase, yeast type)
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.8212.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.5e-251  820.6   0.1   3.9e-251  820.4   0.1    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_4031  Ga0059261_4031 2-isopropylmalate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_4031  Ga0059261_4031 2-isopropylmalate synthase, yeast type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  820.4   0.1  3.9e-251  3.9e-251       1     559 [.       5     550 ..       5     554 .] 0.98

  Alignments for each domain:
  == domain 1  score: 820.4 bits;  conditional E-value: 3.9e-251
                                 TIGR00970   1 pskkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkeievgf 69 
                                               ps ky+pf +i l++r+wp++ itraprwls+d+rdGnqalidpm++e+k r+f+l++r+G keievgf
  lcl|FitnessBrowser__Korea:Ga0059261_4031   5 PSVKYRPFPPIALPDRQWPNRTITRAPRWLSTDMRDGNQALIDPMDAEKKTRFFDLICRVGIKEIEVGF 73 
                                               899****************************************************************** PP

                                 TIGR00970  70 psasqtdfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdlfrevvfra 138
                                               psa  t+fdf+  ++ ++ ipddvt+qvltq+r +li+ t+e+l+Gak  ivh+yna+s+ +r++vf +
  lcl|FitnessBrowser__Korea:Ga0059261_4031  74 PSAGATEFDFISGLVRDNRIPDDVTVQVLTQARRDLIDTTFESLRGAKTGIVHVYNAVSPAWRKIVFGM 142
                                               ********************************************************************* PP

                                 TIGR00970 139 sreevlalavegsklvrklvkdaaksketrwsfeyspesfsdtelefavevceavkeviepteerpiif 207
                                               +r+ev ++a++++kl r   ++aa +++t+w+f+yspe+fs +e +f+vevc av +v++pt erpiif
  lcl|FitnessBrowser__Korea:Ga0059261_4031 143 DRAEVKQIAIDAAKLLR---DNAAAQPDTDWHFQYSPETFSTAEIDFSVEVCAAVMDVLQPTVERPIIF 208
                                               ************88876...6999********************************************* PP

                                 TIGR00970 208 nlpatvevatpnvyadsieylstniaerekvilslhphndrGtavaaaelGllaGadrieGclfGnGer 276
                                               nlpatve atpn+yad+iey+++ni +r+ v++slh+hndrGt+vaaaelG++aGadr+eGcl+GnGer
  lcl|FitnessBrowser__Korea:Ga0059261_4031 209 NLPATVECATPNIYADQIEYFCRNIPNRDAVVVSLHTHNDRGTGVAAAELGMMAGADRVEGCLLGNGER 277
                                               ********************************************************************* PP

                                 TIGR00970 277 tGnvdlvtlalnlytqGvspnldfsdldeilrvvercnkipvherhpygGdlvvtafsGshqdaikkGl 345
                                               tGn dlvt+a+n+ytqGv+p ldfsd+dei+++ve+c +ipvh+r py+Gdlv+tafsGshqdaikkG+
  lcl|FitnessBrowser__Korea:Ga0059261_4031 278 TGNCDLVTVAMNMYTQGVDPGLDFSDIDEIVKTVEYCTNIPVHPRTPYAGDLVFTAFSGSHQDAIKKGF 346
                                               ********************************************************************* PP

                                 TIGR00970 346 daldkkkaaadtlwkvpylpldpkdvgreyeavirvnsqsGkGGvayvlktdlGldlprrlqiefssvv 414
                                                a++ ++++    w+vpylp+dp d+gr yeavirvnsqsGkGGva+vl +d Gl+lp+rlq +fs+ v
  lcl|FitnessBrowser__Korea:Ga0059261_4031 347 AAQEARNDQ---YWEVPYLPIDPADLGRSYEAVIRVNSQSGKGGVAWVLEQDKGLKLPKRLQADFSRHV 412
                                               **9998877...9******************************************************** PP

                                 TIGR00970 415 kdiadskGkelsskeisdlfkeeyllnveqlerislvdyaveddGteskvitavvkikgekkdieGsGn 483
                                               + +ad   +el++++i+  f e+y l  ++++r++l  y      ++++++ + ++++g+++ ++G Gn
  lcl|FitnessBrowser__Korea:Ga0059261_4031 413 QRVADESSRELNAQDIWATFVETYRL--KHPQRFTLGAYDETRASNGERIFAGSIEVDGVQQSVSGRGN 479
                                               *************************9..8899999998888888888********************** PP

                                 TIGR00970 484 GplsalvdaladllnvdvavadysehalgsGddakaasyvelsvrrasdaekatvwGvGiaedvtsasl 552
                                               G +s++v a+++ + vd+++ady+eha+g G++a+aa+yve         +  tvwGvGi+edv++as+
  lcl|FitnessBrowser__Korea:Ga0059261_4031 480 GLISSVVAAMREGFGVDLDIADYAEHAIGHGSGAQAAAYVECRTA-----DGRTVWGVGIDEDVATASV 543
                                               ****************************************98543.....4559*************** PP

                                 TIGR00970 553 ravlsav 559
                                               ravlsa 
  lcl|FitnessBrowser__Korea:Ga0059261_4031 544 RAVLSAA 550
                                               ****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (564 nodes)
Target sequences:                          1  (554 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: 00:00:00.03
# Mc/sec: 10.21
//
[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