Alignments for a candidate for leuA in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Marinobacter adhaerens HP15

Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate GFF2101 HP15_2055 2-isopropylmalate synthase

Query= SwissProt::P42455
         (616 letters)



>FitnessBrowser__Marino:GFF2101
          Length = 564

 Score =  542 bits (1396), Expect = e-158
 Identities = 280/562 (49%), Positives = 374/562 (66%), Gaps = 21/562 (3%)

Query: 46  VEVEDISLPDRTWPDKKITVAPQWCAVDLRDGNQALIDPMSPERKRRMFELLVQMGFKEI 105
           V  + ++  DR WPDK I  AP WCAVDLRDGNQAL+ PMS  +K RMFELLV++GFKEI
Sbjct: 9   VAFKPVAKTDRRWPDKVIEKAPTWCAVDLRDGNQALVKPMSVAQKTRMFELLVKLGFKEI 68

Query: 106 EVGFPSASQTDFDFVREIIEKGMIPDDVTIQVLVQAREHLIRRTFEACEGAKNVIVHFYN 165
           E+GFP+ASQ DFDF R++IE+  IP+DV IQVL QAR  LI RT+EA  GA+  IVH YN
Sbjct: 69  EIGFPAASQPDFDFCRKLIEENRIPEDVKIQVLTQARPELIERTYEALAGARKAIVHVYN 128

Query: 166 STSILQRNVVFRMDKVQVKKLATDAAELIKTIAQDYPDTNWRWQYSPESFTGTEVEYAKE 225
           STS +QR  VF +D+  ++ +A + A+L++ IA  +P+T W +QYSPESFTGTE+++A E
Sbjct: 129 STSTVQREQVFGLDRDGIRDIAVNGAKLVRDIAARHPETQWTFQYSPESFTGTELDFAAE 188

Query: 226 VVDAVVEVMDPTPENPMIINLPSTVEMITPNVYADSIEWMHRNLNRRDSIILSLHPHNDR 285
           V+DAV EV  P    PMIINLP+TVEM TPNV+AD IEW+  N+ RR+ I +S+H HNDR
Sbjct: 189 VIDAVSEVWRPEEGQPMIINLPATVEMATPNVFADQIEWICDNIQRREHISISVHTHNDR 248

Query: 286 GTGVGAAELGYMAGADRIEGCLFGNGERTGNVCLVTLALNMLTQGVDPQLDFTDIRQIRS 345
           G  V AAEL  MAGADR+EG L GNGERTGN+ LVT+A+N+ +QG+DP LD + + +I  
Sbjct: 249 GCAVAAAELAVMAGADRVEGTLMGNGERTGNMDLVTMAMNLYSQGIDPTLDLSGMAEITE 308

Query: 346 TVEYCNQLRVPERHPYGGDLVFTAFSGSHQDAVNKGLDAMAAKVQPGASSTEVSWEQLRD 405
            VE C ++    RHPY G+LVFTAFSGSHQDA+ K L    A+ + G +           
Sbjct: 309 VVEACTEISTHPRHPYAGELVFTAFSGSHQDAIRKCL----ARRKDGET----------- 353

Query: 406 TEWEVPYLPIDPKDVGRDYEAVIRVNSQSGKGGVAYIMKTDHGLQIPRSMQVEFSTVVQN 465
             W V YLPIDP DVGR YE V+R+NSQSGKGGVAY+++ D+ + +PR +Q+EFS VVQ 
Sbjct: 354 --WNVAYLPIDPFDVGRRYEEVVRINSQSGKGGVAYVLERDYNISLPRWLQIEFSKVVQR 411

Query: 466 VTDAEGGEVNSKAMWDIFATEYLERTAPVEQIALRVENAQTENEDASITAELIHNGKDVT 525
             +  GGE++S  +  +F   YL+  A     ALR  +   + E       +  +   V 
Sbjct: 412 EAETNGGEIDSLTIHRLFEDRYLKVHA---DWALRSYDLHRDEEGVHAEVSVGRDASPVR 468

Query: 526 VDGRGNGPLAAYANALEK-LGIDVEIQEYNQHARTSGDDAEAAAYVLAEVNGRKVWGVGI 584
           +DG G G + A + ALEK  GI + ++ Y++ A   G +A A A +    +G       +
Sbjct: 469 LDGHGLGAVEAVSEALEKRFGISIAVEAYDEFALGEGTNANALACIRLTASGMHCSAAAL 528

Query: 585 AGSITYASLKAVTSAVNRALDV 606
           A   T A+L+A+ SAV +A+ +
Sbjct: 529 AEDTTSATLQALFSAVAQAVGI 550


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: 865
Number of extensions: 37
Number of successful extensions: 3
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: 564
Length adjustment: 37
Effective length of query: 579
Effective length of database: 527
Effective search space:   305133
Effective search space used:   305133
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 GFF2101 HP15_2055 (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.13641.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     2e-217  709.1   0.1   2.3e-217  708.9   0.1    1.0  1  lcl|FitnessBrowser__Marino:GFF2101  HP15_2055 2-isopropylmalate synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF2101  HP15_2055 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  708.9   0.1  2.3e-217  2.3e-217       3     562 ..       6     547 ..       4     549 .. 0.95

  Alignments for each domain:
  == domain 1  score: 708.9 bits;  conditional E-value: 2.3e-217
                           TIGR00970   3 kkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkeievgfpsasqtdf 77 
                                         +ky  fk++  ++r+wpdkvi++ap w++vdlrdGnqal+ pmsv++k r+f+llv++Gfkeie+gfp+asq df
  lcl|FitnessBrowser__Marino:GFF2101   6 RKYVAFKPVAKTDRRWPDKVIEKAPTWCAVDLRDGNQALVKPMSVAQKTRMFELLVKLGFKEIEIGFPAASQPDF 80 
                                         69************************************************************************* PP

                           TIGR00970  78 dfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdlfrevvfrasreevlalavegsk 152
                                         df r++ie++ ip+dv iqvltq+r+eli+rt eal+Ga+kaivh+yn+ts+++re vf  +r+ + ++av+g+k
  lcl|FitnessBrowser__Marino:GFF2101  81 DFCRKLIEENRIPEDVKIQVLTQARPELIERTYEALAGARKAIVHVYNSTSTVQREQVFGLDRDGIRDIAVNGAK 155
                                         *************************************************************************** PP

                           TIGR00970 153 lvrklvkdaaksketrwsfeyspesfsdtelefavevceavkeviepteerpiifnlpatvevatpnvyadsiey 227
                                         lvr +   aa+++et+w+f+yspesf++tel+fa ev +av ev++p e +p+i nlpatve+atpnv+ad+ie+
  lcl|FitnessBrowser__Marino:GFF2101 156 LVRDI---AARHPETQWTFQYSPESFTGTELDFAAEVIDAVSEVWRPEEGQPMIINLPATVEMATPNVFADQIEW 227
                                         **987...678999************************************************************* PP

                           TIGR00970 228 lstniaerekvilslhphndrGtavaaaelGllaGadrieGclfGnGertGnvdlvtlalnlytqGvspnldfsd 302
                                         ++ ni  re++ +s+h+hndrG+avaaael ++aGadr+eG l+GnGertGn+dlvt+a+nly+qG++p ld+s 
  lcl|FitnessBrowser__Marino:GFF2101 228 ICDNIQRREHISISVHTHNDRGCAVAAAELAVMAGADRVEGTLMGNGERTGNMDLVTMAMNLYSQGIDPTLDLSG 302
                                         *************************************************************************** PP

                           TIGR00970 303 ldeilrvvercnkipvherhpygGdlvvtafsGshqdaikkGldaldkkkaaadtlwkvpylpldpkdvgreyea 377
                                         + ei +vve c +i+ h+rhpy+G+lv+tafsGshqdai+k l     +k+     w+v ylp+dp dvgr ye 
  lcl|FitnessBrowser__Marino:GFF2101 303 MAEITEVVEACTEISTHPRHPYAGELVFTAFSGSHQDAIRKCLAR---RKDG--ETWNVAYLPIDPFDVGRRYEE 372
                                         *****************************************9964...3333..57******************* PP

                           TIGR00970 378 virvnsqsGkGGvayvlktdlGldlprrlqiefssvvkdiadskGkelsskeisdlfkeeyllnveqlerislvd 452
                                         v+r+nsqsGkGGvayvl +d+ ++lpr lqiefs+vv+  a+++G+e++s  i  lf++ yl  v+   +++  d
  lcl|FitnessBrowser__Marino:GFF2101 373 VVRINSQSGKGGVAYVLERDYNISLPRWLQIEFSKVVQREAETNGGEIDSLTIHRLFEDRYLK-VHADWALRSYD 446
                                         *************************************************************98.77788888888 PP

                           TIGR00970 453 yaveddGteskvitavvkikg..ekkdieGsGnGplsalvdaladllnvdvavadysehalgsGddakaasyvel 525
                                            +++G     ++a v ++     + ++G G G + a+ +al++ + +++av  y e alg G +a+a + ++l
  lcl|FitnessBrowser__Marino:GFF2101 447 LHRDEEG-----VHAEVSVGRdaSPVRLDGHGLGAVEAVSEALEKRFGISIAVEAYDEFALGEGTNANALACIRL 516
                                         8888888.....5666666550055679*****************************************999988 PP

                           TIGR00970 526 svrrasdaekatvwGvGiaedvtsaslravlsavnra 562
                                         + +              +aed tsa+l+a++sav++a
  lcl|FitnessBrowser__Marino:GFF2101 517 TASGMH------CSAAALAEDTTSATLQALFSAVAQA 547
                                         655443......456789****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (564 nodes)
Target sequences:                          1  (564 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: 8.62
//
[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