Alignments for a candidate for leuA in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Cupriavidus basilensis 4G11

Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate RR42_RS21205 RR42_RS21205 2-isopropylmalate synthase

Query= SwissProt::P42455
         (616 letters)



>FitnessBrowser__Cup4G11:RR42_RS21205
          Length = 565

 Score =  586 bits (1511), Expect = e-172
 Identities = 300/570 (52%), Positives = 387/570 (67%), Gaps = 25/570 (4%)

Query: 37  PVNRYMPFEVEVEDISLPDRTWPDKKITVAPQWCAVDLRDGNQALIDPMSPERKRRMFEL 96
           P  +Y P       + + DRTWP K+IT AP W + DLRDGNQALI+PM+P+RK R FE 
Sbjct: 5   PATKYRPATA----VDIADRTWPAKRITRAPVWMSTDLRDGNQALIEPMNPQRKLRFFEQ 60

Query: 97  LVQMGFKEIEVGFPSASQTDFDFVREIIEKGMIPDDVTIQVLVQAREHLIRRTFEACEGA 156
           LV++G K+IEV FPSASQTDFDFVR +IE+  IPDDVTI VL QARE LIRRT E+  GA
Sbjct: 61  LVKIGLKQIEVAFPSASQTDFDFVRMLIEEDRIPDDVTIVVLTQAREDLIRRTIESVRGA 120

Query: 157 KNVIVHFYNSTSILQRNVVFRMDKVQVKKLATDAAELIKTIAQDYPDTNWRWQYSPESFT 216
              +VH YN  +   R +VF   + +VK++A +   LIK +    P+T W ++YSPE+F+
Sbjct: 121 ARAVVHLYNPIAPAFRRIVFGASREEVKEIALEGTRLIKALTDGMPETAWSYEYSPETFS 180

Query: 217 GTEVEYAKEVVDAVVEVMDPTPENPMIINLPSTVEMITPNVYADSIEWMHRNLNRRDSII 276
            TE++++ EV DAV  +  P P  P+I+NLP+TVE  TPN++AD +EWMHR+L RR  I+
Sbjct: 181 MTELDFSLEVCDAVSAIWQPGPTRPLILNLPTTVECSTPNIFADQVEWMHRHLARRADIV 240

Query: 277 LSLHPHNDRGTGVGAAELGYMAGADRIEGCLFGNGERTGNVCLVTLALNMLTQGVDPQLD 336
           LS+HPHNDRGT V AAEL  MAGADR+EGCLFGNGERTGNV LVTLALN+ TQGVDP LD
Sbjct: 241 LSVHPHNDRGTAVAAAELAVMAGADRVEGCLFGNGERTGNVDLVTLALNLYTQGVDPGLD 300

Query: 337 FTDIRQIRSTVEYCNQLRVPERHPYGGDLVFTAFSGSHQDAVNKGLDAMAAKVQPGASST 396
           F+DI ++R  VE CNQL V  RHPY GDLVFTAFSGSHQDA+ KG     A         
Sbjct: 301 FSDIDEVRQCVEDCNQLPVHPRHPYVGDLVFTAFSGSHQDAIRKGFAQHKA--------- 351

Query: 397 EVSWEQLRDTEWEVPYLPIDPKDVGRDYEAVIRVNSQSGKGGVAYIMKTDHGLQIPRSMQ 456
                   D  WEVPYLPIDP D+GR Y+AVIRVNSQSGKGG+AY+++  HG+ +PR +Q
Sbjct: 352 --------DAIWEVPYLPIDPADLGRSYDAVIRVNSQSGKGGMAYLLEQVHGIYMPRRLQ 403

Query: 457 VEFSTVVQNVTDAEGGEVNSKAMWDIFATEYLERTAPVEQIALRVENAQTENEDASITAE 516
           +EFS  VQ++TD  G E ++  ++ +F  EYLE  AP+  +  ++ +    +    I   
Sbjct: 404 IEFSRAVQSMTDESGLEASADDLYGLFKREYLEHEAPLRYMGHQMVSG--SDGQVEIEVA 461

Query: 517 LIHNGKDVTVDGRGNGPLAAYANALE-KLGIDVEIQEYNQHARTSGDDAEAAAYVLAEVN 575
           L+ +G+ ++  GRGNGP+ A+ + L   L + V + +Y++HA + G +A AA YV   V 
Sbjct: 462 LLRDGEALSARGRGNGPIDAFVSGLNGALDMPVRVMDYHEHALSCGANAAAACYVEVRVG 521

Query: 576 GRKV-WGVGIAGSITYASLKAVTSAVNRAL 604
                +G GI  SI  ASLKAV S VNR L
Sbjct: 522 DSATGFGAGIDASIVTASLKAVVSGVNRHL 551


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: 923
Number of extensions: 44
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: 565
Length adjustment: 37
Effective length of query: 579
Effective length of database: 528
Effective search space:   305712
Effective search space used:   305712
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 RR42_RS21205 RR42_RS21205 (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.13901.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-240  785.6   0.0   1.6e-240  785.4   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS21205  RR42_RS21205 2-isopropylmalate s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS21205  RR42_RS21205 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  785.4   0.0  1.6e-240  1.6e-240       1     561 [.       5     549 ..       5     552 .. 0.97

  Alignments for each domain:
  == domain 1  score: 785.4 bits;  conditional E-value: 1.6e-240
                                 TIGR00970   1 pskkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkeievgf 69 
                                               p+ ky+p +a+ +++r+wp k+itrap w+s+dlrdGnqali+pm+++rk r+f++lv+iG k+iev+f
  lcl|FitnessBrowser__Cup4G11:RR42_RS21205   5 PATKYRPATAVDIADRTWPAKRITRAPVWMSTDLRDGNQALIEPMNPQRKLRFFEQLVKIGLKQIEVAF 73 
                                               889****************************************************************** PP

                                 TIGR00970  70 psasqtdfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdlfrevvfra 138
                                               psasqtdfdfvr +ie+  ipddvti vltq+re+li+rt+e+++Ga +a+vhlyn  ++ fr++vf a
  lcl|FitnessBrowser__Cup4G11:RR42_RS21205  74 PSASQTDFDFVRMLIEEDRIPDDVTIVVLTQAREDLIRRTIESVRGAARAVVHLYNPIAPAFRRIVFGA 142
                                               ********************************************************************* PP

                                 TIGR00970 139 sreevlalavegsklvrklvkdaaksketrwsfeyspesfsdtelefavevceavkeviepteerpiif 207
                                               sreev ++a+eg++l+++l++     +et ws+eyspe+fs tel+f++evc+av  +++p + rp+i+
  lcl|FitnessBrowser__Cup4G11:RR42_RS21205 143 SREEVKEIALEGTRLIKALTDG---MPETAWSYEYSPETFSMTELDFSLEVCDAVSAIWQPGPTRPLIL 208
                                               *******************986...578***************************************** PP

                                 TIGR00970 208 nlpatvevatpnvyadsieylstniaerekvilslhphndrGtavaaaelGllaGadrieGclfGnGer 276
                                               nlp+tve +tpn++ad++e++ +++a r  ++ls+hphndrGtavaaael ++aGadr+eGclfGnGer
  lcl|FitnessBrowser__Cup4G11:RR42_RS21205 209 NLPTTVECSTPNIFADQVEWMHRHLARRADIVLSVHPHNDRGTAVAAAELAVMAGADRVEGCLFGNGER 277
                                               ********************************************************************* PP

                                 TIGR00970 277 tGnvdlvtlalnlytqGvspnldfsdldeilrvvercnkipvherhpygGdlvvtafsGshqdaikkGl 345
                                               tGnvdlvtlalnlytqGv+p ldfsd+de+++ ve+cn++pvh+rhpy Gdlv+tafsGshqdai+kG+
  lcl|FitnessBrowser__Cup4G11:RR42_RS21205 278 TGNVDLVTLALNLYTQGVDPGLDFSDIDEVRQCVEDCNQLPVHPRHPYVGDLVFTAFSGSHQDAIRKGF 346
                                               ********************************************************************* PP

                                 TIGR00970 346 daldkkkaaadtlwkvpylpldpkdvgreyeavirvnsqsGkGGvayvlktdlGldlprrlqiefssvv 414
                                                 +     +ad++w+vpylp+dp d+gr y+avirvnsqsGkGG+ay+l + +G+ +prrlqiefs++v
  lcl|FitnessBrowser__Cup4G11:RR42_RS21205 347 AQH-----KADAIWEVPYLPIDPADLGRSYDAVIRVNSQSGKGGMAYLLEQVHGIYMPRRLQIEFSRAV 410
                                               744.....35789******************************************************** PP

                                 TIGR00970 415 kdiadskGkelsskeisdlfkeeyllnveqlerislvdyaveddGteskvitavvkikgekkdieGsGn 483
                                               + ++d  G e s+++++ lfk eyl   e + r+  ++    +dG  +  i+  +  +ge     G Gn
  lcl|FitnessBrowser__Cup4G11:RR42_RS21205 411 QSMTDESGLEASADDLYGLFKREYLE-HEAPLRYMGHQMVSGSDG--QVEIEVALLRDGEALSARGRGN 476
                                               ************************98.667777778888888888..56677777889999******** PP

                                 TIGR00970 484 GplsalvdaladllnvdvavadysehalgsGddakaasyvelsvrrasdaekatvwGvGiaedvtsasl 552
                                               Gp+ a+v  l+  l++ v v+dy ehal++G +a aa+yve+ v  ++     t +G Gi++++ +asl
  lcl|FitnessBrowser__Cup4G11:RR42_RS21205 477 GPIDAFVSGLNGALDMPVRVMDYHEHALSCGANAAAACYVEVRVGDSA-----TGFGAGIDASIVTASL 540
                                               ******************************************998776.....89************** PP

                                 TIGR00970 553 ravlsavnr 561
                                               +av+s+vnr
  lcl|FitnessBrowser__Cup4G11:RR42_RS21205 541 KAVVSGVNR 549
                                               ********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (564 nodes)
Target sequences:                          1  (565 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: 10.57
//
[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:

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