Alignments for a candidate for leuA in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Pseudomonas putida KT2440

Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate PP_1025 PP_1025 2-isopropylmalate synthase

Query= SwissProt::P42455
         (616 letters)



>FitnessBrowser__Putida:PP_1025
          Length = 557

 Score =  610 bits (1574), Expect = e-179
 Identities = 323/570 (56%), Positives = 399/570 (70%), Gaps = 29/570 (5%)

Query: 37  PVNRYMPFEVEVEDISLPDRTWPDKKITVAPQWCAVDLRDGNQALIDPMSPERKRRMFEL 96
           P  +Y  F      I LPDRTWP K IT AP WC+ DLRDGNQ+LI+PM  E+K R ++ 
Sbjct: 7   PSKKYRAFPT----IDLPDRTWPSKTITQAPIWCSSDLRDGNQSLIEPMDSEKKLRFWKT 62

Query: 97  LVQMGFKEIEVGFPSASQTDFDFVREIIEKGMIPDDVTIQVLVQAREHLIRRTFEACEGA 156
           LVQ+G KEIE  FPSASQTDFDFVR +IE G IPDD TIQVL QARE LI RTFE+  GA
Sbjct: 63  LVQVGVKEIEASFPSASQTDFDFVRTLIEDGHIPDDTTIQVLTQAREDLIARTFESLRGA 122

Query: 157 KNVIVHFYNSTSILQRNVVFRMDKVQVKKLATDAAELIKTIAQDYPDTNWRWQYSPESFT 216
           K  IVH YN+TS   R +VF  DK  VK +A +AA+L    A   P+T W +QYSPE+F+
Sbjct: 123 KKAIVHLYNATSPSFRRIVFNQDKQGVKDIAVNAAKLFVKYAAQQPETQWTFQYSPETFS 182

Query: 217 GTEVEYAKEVVDAVVEVMDPTPENPMIINLPSTVEMITPNVYADSIEWMHRNLNRRDSII 276
            TE+E+AKEV DAV+EV +PTPE+ +I+NLP+TVE+ TPN+YAD IEW  RN++RRDS+I
Sbjct: 183 ATEMEFAKEVCDAVIEVWNPTPEHKIILNLPATVEVSTPNIYADQIEWFCRNVSRRDSVI 242

Query: 277 LSLHPHNDRGTGVGAAELGYMAGADRIEGCLFGNGERTGNVCLVTLALNMLTQGVDPQLD 336
           +SLH HNDRGTG+ A ELG MAGADR EGCLFGNGERTGNV LVTLALN+ TQG+DP LD
Sbjct: 243 ISLHCHNDRGTGIAATELGLMAGADRAEGCLFGNGERTGNVDLVTLALNLYTQGIDPLLD 302

Query: 337 FTDIRQIRSTVEYCNQLRVPERHPYGGDLVFTAFSGSHQDAVNKGLDAMAAKVQPGASST 396
           F+DI  +R  VE CNQL V  RHPY GDLV TAFSGSHQDA+ KG     AK Q G    
Sbjct: 303 FSDIDGVRKVVEECNQLPVHPRHPYVGDLVHTAFSGSHQDAIRKGF----AKQQDGEL-- 356

Query: 397 EVSWEQLRDTEWEVPYLPIDPKDVGRDYEAVIRVNSQSGKGGVAYIMKTDHGLQIPRSMQ 456
                      WEVPYLPIDP D+GR YEAVIRVNSQSGKGG+ Y+++ ++G+ +PR MQ
Sbjct: 357 -----------WEVPYLPIDPADIGRSYEAVIRVNSQSGKGGITYLLEQEYGISLPRRMQ 405

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

Query: 517 LIHNGK-DVTVDGRGNGPLAAYANALEKLGIDVEIQEYNQHARTSGDDAEAAAYV-LAEV 574
           +   G+  +   G+GNG L A    L    I VEI +YN+HA  +G +A+AAAY+ L   
Sbjct: 463 VAGEGETTLHWRGKGNGALEALVAGLP---IAVEIMDYNEHAIGAGTNAKAAAYIELRVA 519

Query: 575 NGRKVWGVGIAGSITYASLKAVTSAVNRAL 604
            GR V GVGI  +IT AS KA+ SA+NR+L
Sbjct: 520 GGRPVHGVGIDENITTASFKALFSALNRSL 549


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: 921
Number of extensions: 38
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: 557
Length adjustment: 37
Effective length of query: 579
Effective length of database: 520
Effective search space:   301080
Effective search space used:   301080
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 PP_1025 PP_1025 (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.7971.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   4.9e-244  797.0   0.0   5.7e-244  796.7   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_1025  PP_1025 2-isopropylmalate syntha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_1025  PP_1025 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  796.7   0.0  5.7e-244  5.7e-244       1     562 [.       7     548 ..       7     550 .. 0.95

  Alignments for each domain:
  == domain 1  score: 796.7 bits;  conditional E-value: 5.7e-244
                           TIGR00970   1 pskkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkeievgfpsasqt 75 
                                         pskky+ f +i l++r+wp k it+ap w+s dlrdGnq+li+pm++e+k r++k lv++G keie +fpsasqt
  lcl|FitnessBrowser__Putida:PP_1025   7 PSKKYRAFPTIDLPDRTWPSKTITQAPIWCSSDLRDGNQSLIEPMDSEKKLRFWKTLVQVGVKEIEASFPSASQT 81 
                                         99************************************************************************* PP

                           TIGR00970  76 dfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdlfrevvfrasreevlalaveg 150
                                         dfdfvr +ie+g ipdd tiqvltq+re+li rt+e+l+Gakkaivhlynats+ fr++vf+++++ v ++av++
  lcl|FitnessBrowser__Putida:PP_1025  82 DFDFVRTLIEDGHIPDDTTIQVLTQAREDLIARTFESLRGAKKAIVHLYNATSPSFRRIVFNQDKQGVKDIAVNA 156
                                         *************************************************************************** PP

                           TIGR00970 151 sklvrklvkdaaksketrwsfeyspesfsdtelefavevceavkeviepteerpiifnlpatvevatpnvyadsi 225
                                         +kl    vk aa+++et+w+f+yspe+fs te+efa+evc+av ev++pt+e+ ii+nlpatvev+tpn+yad+i
  lcl|FitnessBrowser__Putida:PP_1025 157 AKL---FVKYAAQQPETQWTFQYSPETFSATEMEFAKEVCDAVIEVWNPTPEHKIILNLPATVEVSTPNIYADQI 228
                                         665...6889999************************************************************** PP

                           TIGR00970 226 eylstniaerekvilslhphndrGtavaaaelGllaGadrieGclfGnGertGnvdlvtlalnlytqGvspnldf 300
                                         e++++n++ r++vi+slh+hndrGt++aa+elGl+aGadr eGclfGnGertGnvdlvtlalnlytqG++p ldf
  lcl|FitnessBrowser__Putida:PP_1025 229 EWFCRNVSRRDSVIISLHCHNDRGTGIAATELGLMAGADRAEGCLFGNGERTGNVDLVTLALNLYTQGIDPLLDF 303
                                         *************************************************************************** PP

                           TIGR00970 301 sdldeilrvvercnkipvherhpygGdlvvtafsGshqdaikkGldaldkkkaaadtlwkvpylpldpkdvgrey 375
                                         sd+d +++vve+cn++pvh+rhpy Gdlv+tafsGshqdai+kG+  ++        lw+vpylp+dp d+gr y
  lcl|FitnessBrowser__Putida:PP_1025 304 SDIDGVRKVVEECNQLPVHPRHPYVGDLVHTAFSGSHQDAIRKGFAKQQ-----DGELWEVPYLPIDPADIGRSY 373
                                         ********************************************97443.....3469***************** PP

                           TIGR00970 376 eavirvnsqsGkGGvayvlktdlGldlprrlqiefssvvkdiadskGkelsskeisdlfkeeyllnveqlerisl 450
                                         eavirvnsqsGkGG++y+l +++G++lprr+qiefs+vv+  +d  G e+++++i+ l+++eyl ++ ++  +s 
  lcl|FitnessBrowser__Putida:PP_1025 374 EAVIRVNSQSGKGGITYLLEQEYGISLPRRMQIEFSQVVQGETDRLGLEMTAQQIYSLLHKEYLQANAPYALVSH 448
                                         *****************************************************************8888877665 PP

                           TIGR00970 451 vdyaveddGteskvitavvkikgekk.dieGsGnGplsalvdaladllnvdvavadysehalgsGddakaasyve 524
                                         +    e++G  + +++  v  +ge++ +  G GnG l alv  l     + v+++dy+eha+g+G +akaa+y+e
  lcl|FitnessBrowser__Putida:PP_1025 449 RL--QEENG--HSAVEVEVAGEGETTlHWRGKGNGALEALVAGLP----IAVEIMDYNEHAIGAGTNAKAAAYIE 515
                                         43..46677..5566666666665542699*********999875....788*********************** PP

                           TIGR00970 525 lsvrrasdaekatvwGvGiaedvtsaslravlsavnra 562
                                         l v          v GvGi+e++t+as++a++sa+nr 
  lcl|FitnessBrowser__Putida:PP_1025 516 LRVAGGR-----PVHGVGIDENITTASFKALFSALNRS 548
                                         *998776.....589*********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (564 nodes)
Target sequences:                          1  (557 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: 12.30
//
[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