Alignments for a candidate for leuA in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Burkholderia phytofirmans PsJN

Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate BPHYT_RS13280 BPHYT_RS13280 2-isopropylmalate synthase

Query= SwissProt::P42455
         (616 letters)



>FitnessBrowser__BFirm:BPHYT_RS13280
          Length = 572

 Score =  600 bits (1547), Expect = e-176
 Identities = 311/571 (54%), Positives = 395/571 (69%), Gaps = 33/571 (5%)

Query: 37  PVNRYMPFEVEVEDISLPDRTWPDKKITVAPQWCAVDLRDGNQALIDPMSPERKRRMFEL 96
           P  +Y  F+     ++L DR WP + IT  P W + DLRDGNQ+L +PM  +RK RMF+ 
Sbjct: 5   PATKYRSFK----PVTLTDRQWPSRTITHPPIWMSTDLRDGNQSLFEPMDAQRKMRMFKT 60

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

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

Query: 217 GTEVEYAKEVVDAVVEVMDPTPENPMIINLPSTVEMITPNVYADSIEWMHRNLNRRDSII 276
           GTE+E+AKEV DAV +V  PTPE+  I+NLP+TVEM TPN+YAD IEWMHRNL RRDS+I
Sbjct: 181 GTEIEFAKEVCDAVFDVWQPTPEHKAIVNLPATVEMSTPNIYADQIEWMHRNLARRDSLI 240

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

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

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

Query: 457 VEFSTVVQNVTDAEGGEVNSKAMWDIFATEYLERTAPVEQIALRVENAQTENEDASITAE 516
           V+FS+ VQ  TD  G EV S  +W++F  EY++ TAP+  +   +   +   E   +T +
Sbjct: 404 VDFSSAVQRFTDDSGQEVTSAQIWELFQQEYVQNTAPIHYVGHSLSERE-GRERIKLTVD 462

Query: 517 LIHNGKDVTVDGRGNGPLAAYANALEKLGIDVEIQEYNQHARTSGDDAEAAAYVLAEVNG 576
           +  +G    + G GNGPL A  +A   +G+ V IQ Y + A T G DA A A  +AE+ G
Sbjct: 463 I--HGTRRVLTGEGNGPLDALMHA---IGVPVRIQHYEERALTQGADARAVA--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: 924
Number of extensions: 38
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 BPHYT_RS13280 BPHYT_RS13280 (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.32338.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   7.8e-237  773.2   0.0   9.4e-237  772.9   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS13280  BPHYT_RS13280 2-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS13280  BPHYT_RS13280 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  772.9   0.0  9.4e-237  9.4e-237       1     562 [.       5     546 ..       5     548 .. 0.96

  Alignments for each domain:
  == domain 1  score: 772.9 bits;  conditional E-value: 9.4e-237
                                TIGR00970   1 pskkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkeievgfp 70 
                                              p+ ky+ fk++ l++r+wp + it+ p w+s+dlrdGnq+l +pm+++rk r+fk lv+iGfkeiev+fp
  lcl|FitnessBrowser__BFirm:BPHYT_RS13280   5 PATKYRSFKPVTLTDRQWPSRTITHPPIWMSTDLRDGNQSLFEPMDAQRKMRMFKTLVQIGFKEIEVAFP 74 
                                              889******************************************************************* PP

                                TIGR00970  71 sasqtdfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdlfrevvfrasr 140
                                              sasqtdf+fvre+ie g ipddvti+vltq+r++li+rt+e+l+G ++aivhlynat++ fr++vf+ ++
  lcl|FitnessBrowser__BFirm:BPHYT_RS13280  75 SASQTDFNFVRELIEGGHIPDDVTIEVLTQARDDLIERTFESLRGVPRAIVHLYNATAPEFRKIVFNLEK 144
                                              ********************************************************************** PP

                                TIGR00970 141 eevlalavegsklvrklvkdaaksketrwsfeyspesfsdtelefavevceavkeviepteerpiifnlp 210
                                                v +la ++   +r + + aa  +et+++f+yspe fs+te efa+evc+av +v++pt+e+  i nlp
  lcl|FitnessBrowser__BFirm:BPHYT_RS13280 145 SGVKELAQNA---ARTMKRIAATMPETQFTFQYSPEVFSGTEIEFAKEVCDAVFDVWQPTPEHKAIVNLP 211
                                              **********...788888899************************************************ PP

                                TIGR00970 211 atvevatpnvyadsieylstniaerekvilslhphndrGtavaaaelGllaGadrieGclfGnGertGnv 280
                                              atve++tpn+yad+ie++ +n+a r+++i+s+hphndrGtavaaael ++aGadrieGclfGnGertGnv
  lcl|FitnessBrowser__BFirm:BPHYT_RS13280 212 ATVEMSTPNIYADQIEWMHRNLARRDSLIISVHPHNDRGTAVAAAELAVMAGADRIEGCLFGNGERTGNV 281
                                              ********************************************************************** PP

                                TIGR00970 281 dlvtlalnlytqGvspnldfsdldeilrvvercnkipvherhpygGdlvvtafsGshqdaikkGldaldk 350
                                              dlvtlalnlytqGv+p ldfs+++e+ r+ e+c ++p+h+rhpy Gdlv+tafsGshqdaikkG+ +++ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS13280 282 DLVTLALNLYTQGVDPGLDFSNINEVARTAEECTQLPIHPRHPYVGDLVFTAFSGSHQDAIKKGFAVQKP 351
                                              *****************************************************************99864 PP

                                TIGR00970 351 kkaaadtlwkvpylpldpkdvgreyeavirvnsqsGkGGvayvlktdlGldlprrlqiefssvvkdiads 420
                                                   d++w+vpy+p+dp d+gr+y++virvnsqsGkGG+ay+l + +G+ lprrlq++fss+v+ ++d 
  lcl|FitnessBrowser__BFirm:BPHYT_RS13280 352 -----DAVWEVPYMPIDPADLGRTYDSVIRVNSQSGKGGIAYLLEQGYGVVLPRRLQVDFSSAVQRFTDD 416
                                              .....679************************************************************** PP

                                TIGR00970 421 kGkelsskeisdlfkeeyllnveqlerislvdyaveddGteskvitavvkikgekkdieGsGnGplsalv 490
                                               G+e++s +i++lf++ey  n+ +++    v +++++   +++ i+ +v+i+g+++ + G GnGpl al+
  lcl|FitnessBrowser__BFirm:BPHYT_RS13280 417 SGQEVTSAQIWELFQQEYVQNTAPIH---YVGHSLSERE-GRERIKLTVDIHGTRRVLTGEGNGPLDALM 482
                                              ******************99766655...5555555544.5889**********************9999 PP

                                TIGR00970 491 daladllnvdvavadysehalgsGddakaasyvelsvrrasdaekatvwGvGiaedvtsaslravlsavn 560
                                              +a+     v v + +y e al+ G da+a +  e++         +  +GvGi++++ +as+rav+s+vn
  lcl|FitnessBrowser__BFirm:BPHYT_RS13280 483 HAIG----VPVRIQHYEERALTQGADARAVAVAEMAGADV----TGSAFGVGIDANLVTASIRAVISGVN 544
                                              9974....7789*****************99888765544....5899********************** PP

                                TIGR00970 561 ra 562
                                              ra
  lcl|FitnessBrowser__BFirm:BPHYT_RS13280 545 RA 546
                                              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: 7.58
//
[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