GapMind for Amino acid biosynthesis

 

Aligments for a candidate for leuA in Cupriavidus basilensis 4G11

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

Query= BRENDA::P9WQB3
         (644 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS21205 RR42_RS21205
           2-isopropylmalate synthase
          Length = 565

 Score =  585 bits (1507), Expect = e-171
 Identities = 311/601 (51%), Positives = 392/601 (65%), Gaps = 57/601 (9%)

Query: 42  PVNRYRPFAEEVEPIRLRNRTWPDRVIDRAPLWCAVDLRDGNQALIDPMSPARKRRMFDL 101
           P  +YRP       + + +RTWP + I RAP+W + DLRDGNQALI+PM+P RK R F+ 
Sbjct: 5   PATKYRP----ATAVDIADRTWPAKRITRAPVWMSTDLRDGNQALIEPMNPQRKLRFFEQ 60

Query: 102 LVRMGYKEIEVGFPSASQTDFDFVREIIEQGAIPDDVTIQVLTQCRPELIERTFQACSGA 161
           LV++G K+IEV FPSASQTDFDFVR +IE+  IPDDVTI VLTQ R +LI RT ++  GA
Sbjct: 61  LVKIGLKQIEVAFPSASQTDFDFVRMLIEEDRIPDDVTIVVLTQAREDLIRRTIESVRGA 120

Query: 162 PRAIVHFYNSTSILQRRVVFRANRAEVQAIATDGARKCVEQAAKYPGTQWRFEYSPESYT 221
            RA+VH YN  +   RR+VF A+R EV+ IA +G R         P T W +EYSPE+++
Sbjct: 121 ARAVVHLYNPIAPAFRRIVFGASREEVKEIALEGTRLIKALTDGMPETAWSYEYSPETFS 180

Query: 222 GTELEYAKQVCDAVGEVIAPTPERPIIFNLPATVEMTTPNVYADSIEWMSRNLANRESVI 281
            TEL+++ +VCDAV  +  P P RP+I NLP TVE +TPN++AD +EWM R+LA R  ++
Sbjct: 181 MTELDFSLEVCDAVSAIWQPGPTRPLILNLPTTVECSTPNIFADQVEWMHRHLARRADIV 240

Query: 282 LSLHPHNDRGTAVAAAELGFAAGADRIEGCLFGNGERTGNVCLVTLGLNLFSRGVDPQID 341
           LS+HPHNDRGTAVAAAEL   AGADR+EGCLFGNGERTGNV LVTL LNL+++GVDP +D
Sbjct: 241 LSVHPHNDRGTAVAAAELAVMAGADRVEGCLFGNGERTGNVDLVTLALNLYTQGVDPGLD 300

Query: 342 FSNIDEIRRTVEYCNQLPVHERHPYGGDLVYTAFSGSHQDAINKGLDAMKLDADAADCDV 401
           FS+IDE+R+ VE CNQLPVH RHPY GDLV+TAFSGSHQDAI KG    K DA       
Sbjct: 301 FSDIDEVRQCVEDCNQLPVHPRHPYVGDLVFTAFSGSHQDAIRKGFAQHKADA------- 353

Query: 402 DDMLWQVPYLPIDPRDVGRTYEAVIRVNSQSGKGGVAYIMKTDHGLSLPRRLQIEFSQVI 461
              +W+VPYLPIDP D+GR+Y+AVIRVNSQSGKGG+AY+++  HG+ +PRRLQIEFS+ +
Sbjct: 354 ---IWEVPYLPIDPADLGRSYDAVIRVNSQSGKGGMAYLLEQVHGIYMPRRLQIEFSRAV 410

Query: 462 QKIAEGTAGEGGEVSPKEMWDAFAEEYLAPVRPLERIRQHVDAADDDGGTTSITATVKIN 521
           Q +   T   G E S  +++  F  EYL    PL  +   + +  D  G   I   +  +
Sbjct: 411 QSM---TDESGLEASADDLYGLFKREYLEHEAPLRYMGHQMVSGSD--GQVEIEVALLRD 465

Query: 522 GVETEISGSGNGPLAAFVHAL-ADVGFDVAVLDYYEHAMSAGDDAQAAAYVEASVTIASP 580
           G      G GNGP+ AFV  L   +   V V+DY+EHA+S G +A AA YVE  V     
Sbjct: 466 GEALSARGRGNGPIDAFVSGLNGALDMPVRVMDYHEHALSCGANAAAACYVEVRVG---- 521

Query: 581 AQPGEAGRHASDPVTIASPAQPGEAGRHASDPVTSKTVWGVGIAPSITTASLRAVVSAVN 640
                                             S T +G GI  SI TASL+AVVS VN
Sbjct: 522 ---------------------------------DSATGFGAGIDASIVTASLKAVVSGVN 548

Query: 641 R 641
           R
Sbjct: 549 R 549


Lambda     K      H
   0.317    0.133    0.399 

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: 939
Number of extensions: 37
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: 644
Length of database: 565
Length adjustment: 37
Effective length of query: 607
Effective length of database: 528
Effective search space:   320496
Effective search space used:   320496
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 (21.7 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.27730.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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.03
# Mc/sec: 8.01
//
[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 preprint 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