Alignments for a candidate for leuA in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Acidovorax sp. GW101-3H11

Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate Ac3H11_5000 2-isopropylmalate synthase (EC 2.3.3.13)

Query= SwissProt::P42455
         (616 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_5000
          Length = 566

 Score =  545 bits (1404), Expect = e-159
 Identities = 281/570 (49%), Positives = 370/570 (64%), Gaps = 29/570 (5%)

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

Query: 97  LVQMGFKEIEVGFPSASQTDFDFVREIIEKGMIPDDVTIQVLVQAREHLIRRTFEACEGA 156
           LV++GFKEIEVGFP+ASQTDFDFVR +I++ +IPDDVT+ V+ Q+RE LI RT EA +GA
Sbjct: 61  LVRIGFKEIEVGFPAASQTDFDFVRRLIDENLIPDDVTLMVMTQSREDLIARTVEAVQGA 120

Query: 157 KNVIVHFYNSTSILQRNVVFRMDKVQVKKLATDAAELIKTIAQDYPDTNWRWQYSPESFT 216
              IVH YN+T+   R +VF M+  QV +L       +K +    P+T W  QYSPE+F+
Sbjct: 121 PRAIVHLYNATAPAWRRIVFGMNVTQVMQLIAHHVGYLKQLTDTQPETQWTLQYSPETFS 180

Query: 217 GTEVEYAKEVVDAVVEVMDPTPENPMIINLPSTVEMITPNVYADSIEWMHRNLNRRDSII 276
            TE+  + +     +   +  P  P+IINLP+TVE  TPNV+AD IEWM R+L  R+ I+
Sbjct: 181 ATELSVSLKACQTAIAAWNAGPGRPIIINLPTTVENATPNVFADQIEWMDRHLAPREHIV 240

Query: 277 LSLHPHNDRGTGVGAAELGYMAGADRIEGCLFGNGERTGNVCLVTLALNMLTQGVDPQLD 336
           LS+HPHNDRGTGV AAEL  MAGADR+EGCLFGNGER GNV +VTLALN+ TQGV P LD
Sbjct: 241 LSVHPHNDRGTGVAAAELAMMAGADRVEGCLFGNGERCGNVDIVTLALNLYTQGVHPNLD 300

Query: 337 FTDIRQIRSTVEYCNQLRVPERHPYGGDLVFTAFSGSHQDAVNKGLDAMAAKVQPGASST 396
           F+DI  +    E C  L V  RHPY GDLVFTAFSGSHQDA+ KG  A      P A   
Sbjct: 301 FSDITSVARIAEECTSLPVHPRHPYAGDLVFTAFSGSHQDAIKKGFAAQ----DPNAL-- 354

Query: 397 EVSWEQLRDTEWEVPYLPIDPKDVGRDYEAVIRVNSQSGKGGVAYIMKTDHGLQIPRSMQ 456
                      WEVPYLPIDP D+GR Y++VIRVNSQSGKGG+A++++ +HG+ +PR MQ
Sbjct: 355 -----------WEVPYLPIDPADLGRTYDSVIRVNSQSGKGGIAFLLEREHGVVMPRRMQ 403

Query: 457 VEFSTVVQNVTDAEGGEVNSKAMWDIFATEYLERTAPVEQIALRVENAQTENEDASITAE 516
           VEFS VVQ  TDA  GE+   A+W +F   YL   A   Q A+   + + + +   I  +
Sbjct: 404 VEFSAVVQRQTDASEGEMTGDALWSLFQATYLRAPA---QAAITCHSHKLDEDGQGIELD 460

Query: 517 LIHNGKDVTVDGRGNGPLAAYANALEKLGIDVEIQEYNQHARTSGDDAEAAAYVLAEVNG 576
           +  +G   T+ G+GNGP+AA  +A   LG+ + +  Y + A  +G +A+A A V A + G
Sbjct: 461 VTIDGTRQTLRGQGNGPIAATVDA---LGLPLRVDHYEERATGTGANAQALAIVEAAMEG 517

Query: 577 --RKVWGVGIAGSITYASLKAVTSAVNRAL 604
                +G G + +I  AS+ A+    NR +
Sbjct: 518 VAGATFGAGASHNIVTASVLAIVGVANRLM 547


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: 896
Number of extensions: 38
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: 566
Length adjustment: 37
Effective length of query: 579
Effective length of database: 529
Effective search space:   306291
Effective search space used:   306291
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 Ac3H11_5000 (2-isopropylmalate synthase (EC 2.3.3.13))
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.15302.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   1.1e-224  733.0   0.0   1.4e-224  732.7   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_5000  2-isopropylmalate synthase (EC 2


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_5000  2-isopropylmalate synthase (EC 2.3.3.13)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  732.7   0.0  1.4e-224  1.4e-224       1     562 [.       5     546 ..       5     548 .. 0.97

  Alignments for each domain:
  == domain 1  score: 732.7 bits;  conditional E-value: 1.4e-224
                                        TIGR00970   1 pskkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGf 62 
                                                      p+ ky+p ++i l++r+wp + itraprwls+dlrdGnqal +pm++erk ++f  lvriGf
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_5000   5 PATKYQPIAPIALADRQWPSRSITRAPRWLSTDLRDGNQALFEPMNGERKMKLFAELVRIGF 66 
                                                      889*********************************************************** PP

                                        TIGR00970  63 keievgfpsasqtdfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhly 124
                                                      keievgfp+asqtdfdfvr++i+++lipddvt+ v+tqsre+li rtvea++Ga++aivhly
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_5000  67 KEIEVGFPAASQTDFDFVRRLIDENLIPDDVTLMVMTQSREDLIARTVEAVQGAPRAIVHLY 128
                                                      ************************************************************** PP

                                        TIGR00970 125 natsdlfrevvfrasreevlalavegsklvrklvkdaaksketrwsfeyspesfsdtelefa 186
                                                      nat++ +r++vf ++  +v++l  +     ++l+     ++et+w+ +yspe+fs tel  +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_5000 129 NATAPAWRRIVFGMNVTQVMQLIAHHVGYLKQLT---DTQPETQWTLQYSPETFSATELSVS 187
                                                      ********************99998855555555...56889******************** PP

                                        TIGR00970 187 vevceavkeviepteerpiifnlpatvevatpnvyadsieylstniaerekvilslhphndr 248
                                                      ++ c++   +++  + rpii nlp+tve atpnv+ad+ie++ +++a re+++ls+hphndr
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_5000 188 LKACQTAIAAWNAGPGRPIIINLPTTVENATPNVFADQIEWMDRHLAPREHIVLSVHPHNDR 249
                                                      ************************************************************** PP

                                        TIGR00970 249 GtavaaaelGllaGadrieGclfGnGertGnvdlvtlalnlytqGvspnldfsdldeilrvv 310
                                                      Gt+vaaael ++aGadr+eGclfGnGer Gnvd+vtlalnlytqGv pnldfsd++++ r+ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_5000 250 GTGVAAAELAMMAGADRVEGCLFGNGERCGNVDIVTLALNLYTQGVHPNLDFSDITSVARIA 311
                                                      ************************************************************** PP

                                        TIGR00970 311 ercnkipvherhpygGdlvvtafsGshqdaikkGldaldkkkaaadtlwkvpylpldpkdvg 372
                                                      e+c  +pvh+rhpy+Gdlv+tafsGshqdaikkG+ a+d      ++lw+vpylp+dp d+g
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_5000 312 EECTSLPVHPRHPYAGDLVFTAFSGSHQDAIKKGFAAQDP-----NALWEVPYLPIDPADLG 368
                                                      ***********************************99875.....469************** PP

                                        TIGR00970 373 reyeavirvnsqsGkGGvayvlktdlGldlprrlqiefssvvkdiadskGkelsskeisdlf 434
                                                      r+y++virvnsqsGkGG+a++l +++G+ +prr+q+efs vv+  +d+  +e++ + ++ lf
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_5000 369 RTYDSVIRVNSQSGKGGIAFLLEREHGVVMPRRMQVEFSAVVQRQTDASEGEMTGDALWSLF 430
                                                      ************************************************************** PP

                                        TIGR00970 435 keeyllnveqlerislvdyaveddGteskvitavvkikgekkdieGsGnGplsalvdaladl 496
                                                      + +yl     + +i+ +++++++dG   + i+  v i+g+++ + G GnGp++a vdal   
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_5000 431 QATYLR-APAQAAITCHSHKLDEDG---QGIELDVTIDGTRQTLRGQGNGPIAATVDALGL- 487
                                                      ****98.667789************...8899**************************974. PP

                                        TIGR00970 497 lnvdvavadysehalgsGddakaasyvelsvrrasdaekatvwGvGiaedvtsaslravlsa 558
                                                          + v +y e a g+G +a+a + ve++++  +    + ++G G ++++ +as+ a++  
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_5000 488 ---PLRVDHYEERATGTGANAQALAIVEAAMEGVA----GATFGAGASHNIVTASVLAIVGV 542
                                                      ...55889*********************999988....889******************99 PP

                                        TIGR00970 559 vnra 562
                                                       nr 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_5000 543 ANRL 546
                                                      8886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (564 nodes)
Target sequences:                          1  (566 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: 00:00:00.02
# Mc/sec: 10.92
//
[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