Alignments for a candidate for leuA in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Pseudomonas fluorescens GW456-L13

Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate PfGW456L13_4854 2-isopropylmalate synthase (EC 2.3.3.13)

Query= SwissProt::P42455
         (616 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854
          Length = 559

 Score =  608 bits (1567), Expect = e-178
 Identities = 317/572 (55%), Positives = 399/572 (69%), Gaps = 31/572 (5%)

Query: 37  PVNRYMPFEVEVEDISLPDRTWPDKKITVAPQWCAVDLRDGNQALIDPMSPERKRRMFEL 96
           P ++Y  F      I +PDRTWP K IT AP WC+ DLRDGNQ+LI+PM   +K R ++ 
Sbjct: 7   PSSKYRAFPT----IDIPDRTWPSKTITAAPIWCSSDLRDGNQSLIEPMDAVKKLRFWKT 62

Query: 97  LVQMGFKEIEVGFPSASQTDFDFVREIIEKGMIPDDVTIQVLVQAREHLIRRTFEACEGA 156
           LVQ+G KEIE  FP+ASQTDFDFVR +IE   IPDD TIQVL Q RE LI RTFE+  GA
Sbjct: 63  LVQVGVKEIEASFPAASQTDFDFVRTLIEGNHIPDDTTIQVLTQGREDLIERTFESLRGA 122

Query: 157 KNVIVHFYNSTSILQRNVVFRMDKVQVKKLATDAAELIKTIAQDYPDTNWRWQYSPESFT 216
           K  IVH YN+TS   R +VF  DK  VK +A +AA+L    A   PDT W ++YSPE+F+
Sbjct: 123 KKAIVHLYNATSPSFRRIVFNQDKDGVKAIAVNAAKLFVKYAAMQPDTEWTFEYSPETFS 182

Query: 217 GTEVEYAKEVVDAVVEVMDPTPENPMIINLPSTVEMITPNVYADSIEWMHRNLNRRDSII 276
            TE+E+AKEV DAV+EV +PTPE+ MI+NLP+TVE  TPN+YAD IEW  R++NRRDS+I
Sbjct: 183 ATEMEFAKEVCDAVIEVWNPTPEHKMILNLPATVECATPNIYADQIEWFGRHINRRDSVI 242

Query: 277 LSLHPHNDRGTGVGAAELGYMAGADRIEGCLFGNGERTGNVCLVTLALNMLTQGVDPQLD 336
           +SLH HNDRGTGV A ELG MAGADR+EGCLFGNGERTGNV LVT+ALN+ TQGV+P+LD
Sbjct: 243 ISLHTHNDRGTGVAATELGLMAGADRVEGCLFGNGERTGNVDLVTVALNLYTQGVNPELD 302

Query: 337 FTDIRQIRSTVEYCNQLRVPERHPYGGDLVFTAFSGSHQDAVNKGLDAMAAKVQPGASST 396
           F+DI  +R  VE CNQ++V  RHPY GDLV TAFSGSHQDA+ KG               
Sbjct: 303 FSDIDGVRKVVEECNQIQVHPRHPYVGDLVHTAFSGSHQDAIRKGFA------------- 349

Query: 397 EVSWEQLRDTEWEVPYLPIDPKDVGRDYEAVIRVNSQSGKGGVAYIMKTDHGLQIPRSMQ 456
               +Q  D  WEVPYLPIDP D+GR YEAVIRVNSQSGKGG+AY+++ ++G+ +PR MQ
Sbjct: 350 ----QQKPDALWEVPYLPIDPADIGRSYEAVIRVNSQSGKGGIAYLLEQEYGISLPRRMQ 405

Query: 457 VEFSTVVQNVTDAEGGEVNSKAMWDIFATEYLERTAPVEQIALRVENAQTENEDASITAE 516
           +EFS VVQ  TD  G E+ ++ +  +  +EYL+   P   ++ R+   Q EN  +++  E
Sbjct: 406 IEFSQVVQRETDRLGLEMTAQQIHALLHSEYLQANTPYALVSHRL---QEENGHSAVEVE 462

Query: 517 LIHNGKDVT---VDGRGNGPLAAYANALEKLGIDVEIQEYNQHARTSGDDAEAAAYVLAE 573
           +   G+  T     G+GNG L A    L    + VEI +YN+HA  +G +A+AAAY+   
Sbjct: 463 VASQGQGETNLHWRGKGNGALEALVAGLP---VPVEIMDYNEHAIGAGTNAKAAAYIELR 519

Query: 574 VNG-RKVWGVGIAGSITYASLKAVTSAVNRAL 604
           VNG R V GVGI  +IT AS KA+ SA+NR+L
Sbjct: 520 VNGERAVHGVGIDENITTASFKALFSALNRSL 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: 955
Number of extensions: 34
Number of successful extensions: 4
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: 559
Length adjustment: 37
Effective length of query: 579
Effective length of database: 522
Effective search space:   302238
Effective search space used:   302238
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 PfGW456L13_4854 (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.24171.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   1.2e-241  789.1   0.0   1.4e-241  788.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854  2-isopropylmalate synthase (EC 2


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854  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 !  788.8   0.0  1.4e-241  1.4e-241       1     562 [.       7     550 ..       7     552 .. 0.95

  Alignments for each domain:
  == domain 1  score: 788.8 bits;  conditional E-value: 1.4e-241
                                               TIGR00970   1 pskkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfk 55 
                                                             ps+ky+ f +i +++r+wp k it ap w+s dlrdGnq+li+pm++ +k r++k
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854   7 PSSKYRAFPTIDIPDRTWPSKTITAAPIWCSSDLRDGNQSLIEPMDAVKKLRFWK 61 
                                                             99***************************************************** PP

                                               TIGR00970  56 llvriGfkeievgfpsasqtdfdfvreiieqglipddvtiqvltqsreelikrtv 110
                                                              lv++G keie +fp+asqtdfdfvr +ie + ipdd tiqvltq re+li+rt+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854  62 TLVQVGVKEIEASFPAASQTDFDFVRTLIEGNHIPDDTTIQVLTQGREDLIERTF 116
                                                             ******************************************************* PP

                                               TIGR00970 111 ealsGakkaivhlynatsdlfrevvfrasreevlalavegsklvrklvkdaaksk 165
                                                             e+l+Gakkaivhlynats+ fr++vf+++++ v a+av+++kl    vk aa ++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854 117 ESLRGAKKAIVHLYNATSPSFRRIVFNQDKDGVKAIAVNAAKL---FVKYAAMQP 168
                                                             ****************************************665...78899**** PP

                                               TIGR00970 166 etrwsfeyspesfsdtelefavevceavkeviepteerpiifnlpatvevatpnv 220
                                                             +t+w+feyspe+fs te+efa+evc+av ev++pt+e+ +i+nlpatve atpn+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854 169 DTEWTFEYSPETFSATEMEFAKEVCDAVIEVWNPTPEHKMILNLPATVECATPNI 223
                                                             ******************************************************* PP

                                               TIGR00970 221 yadsieylstniaerekvilslhphndrGtavaaaelGllaGadrieGclfGnGe 275
                                                             yad+ie++ ++i  r++vi+slh+hndrGt+vaa+elGl+aGadr+eGclfGnGe
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854 224 YADQIEWFGRHINRRDSVIISLHTHNDRGTGVAATELGLMAGADRVEGCLFGNGE 278
                                                             ******************************************************* PP

                                               TIGR00970 276 rtGnvdlvtlalnlytqGvspnldfsdldeilrvvercnkipvherhpygGdlvv 330
                                                             rtGnvdlvt+alnlytqGv+p+ldfsd+d +++vve+cn+i+vh+rhpy Gdlv+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854 279 RTGNVDLVTVALNLYTQGVNPELDFSDIDGVRKVVEECNQIQVHPRHPYVGDLVH 333
                                                             ******************************************************* PP

                                               TIGR00970 331 tafsGshqdaikkGldaldkkkaaadtlwkvpylpldpkdvgreyeavirvnsqs 385
                                                             tafsGshqdai+kG+  ++      d+lw+vpylp+dp d+gr yeavirvnsqs
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854 334 TAFSGSHQDAIRKGFAQQK-----PDALWEVPYLPIDPADIGRSYEAVIRVNSQS 383
                                                             ***************7654.....4679*************************** PP

                                               TIGR00970 386 GkGGvayvlktdlGldlprrlqiefssvvkdiadskGkelsskeisdlfkeeyll 440
                                                             GkGG+ay+l +++G++lprr+qiefs+vv+  +d  G e+++++i  l++ eyl 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854 384 GKGGIAYLLEQEYGISLPRRMQIEFSQVVQRETDRLGLEMTAQQIHALLHSEYLQ 438
                                                             ******************************************************* PP

                                               TIGR00970 441 nveqlerislvdyaveddGteskvitavvkikge...kkdieGsGnGplsalvda 492
                                                             ++ ++  +s +    e++G  + +++  v  +g+   + +  G GnG l alv  
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854 439 ANTPYALVSHRL--QEENG--HSAVEVEVASQGQgetNLHWRGKGNGALEALVAG 489
                                                             888887776554..46677..344444454444410134589*********9998 PP

                                               TIGR00970 493 ladllnvdvavadysehalgsGddakaasyvelsvrrasdaekatvwGvGiaedv 547
                                                             l     v v+++dy+eha+g+G +akaa+y+el v+ +       v GvGi+e++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854 490 LP----VPVEIMDYNEHAIGAGTNAKAAAYIELRVNGER-----AVHGVGIDENI 535
                                                             75....778************************998766.....799******** PP

                                               TIGR00970 548 tsaslravlsavnra 562
                                                             t+as++a++sa+nr 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4854 536 TTASFKALFSALNRS 550
                                                             *************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (564 nodes)
Target sequences:                          1  (559 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: 9.38
//
[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