Alignments for a candidate for leuA in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Pseudomonas stutzeri RCH2

Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate GFF1244 Psest_1277 2-isopropylmalate synthase, yeast type

Query= SwissProt::P42455
         (616 letters)



>FitnessBrowser__psRCH2:GFF1244
          Length = 556

 Score =  615 bits (1587), Expect = e-180
 Identities = 316/569 (55%), Positives = 405/569 (71%), Gaps = 28/569 (4%)

Query: 37  PVNRYMPFEVEVEDISLPDRTWPDKKITVAPQWCAVDLRDGNQALIDPMSPERKRRMFEL 96
           P  +Y  F      I +PDRTWP K IT AP W + DLRDGNQ+LI+PM   +K R F+ 
Sbjct: 7   PSKKYRAFPA----IDIPDRTWPSKTITQAPIWLSSDLRDGNQSLIEPMDAAKKMRFFKT 62

Query: 97  LVQMGFKEIEVGFPSASQTDFDFVREIIEKGMIPDDVTIQVLVQAREHLIRRTFEACEGA 156
           LVQ+G KEIEVGFPSASQTDFDFVRE+IE G IPDDVTIQVL QARE LI RTFE+ +GA
Sbjct: 63  LVQVGIKEIEVGFPSASQTDFDFVRELIEGGHIPDDVTIQVLTQAREDLITRTFESLKGA 122

Query: 157 KNVIVHFYNSTSILQRNVVFRMDKVQVKKLATDAAELIKTIAQDYPDTNWRWQYSPESFT 216
           K  IVH+YN+T+   R +VF  DK  V  +A +AA++IK +A   P+T WR++YSPE F+
Sbjct: 123 KQAIVHYYNATAPSFRRIVFNQDKAGVVNIAVNAAQIIKRLAAQNPETAWRFEYSPEIFS 182

Query: 217 GTEVEYAKEVVDAVVEVMDPTPENPMIINLPSTVEMITPNVYADSIEWMHRNLNRRDSII 276
            TE E+A EV +AV+EV  PTPE  +I+NLP+TVE  TPN+YAD IEW  R+++RRDS++
Sbjct: 183 STEPEFAVEVCNAVIEVFQPTPEQKLILNLPATVEAATPNIYADQIEWFCRHVDRRDSVL 242

Query: 277 LSLHPHNDRGTGVGAAELGYMAGADRIEGCLFGNGERTGNVCLVTLALNMLTQGVDPQLD 336
           +SLH HNDRGTGV A ELG MAGADR+EGCLFGNGERTGNV LVT+ALNM TQG+DPQLD
Sbjct: 243 VSLHTHNDRGTGVAATELGLMAGADRVEGCLFGNGERTGNVDLVTVALNMYTQGIDPQLD 302

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

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

Query: 457 VEFSTVVQNVTDAEGGEVNSKAMWDIFATEYLERTAPVEQIALRVENAQTENEDASITAE 516
           +EFS VVQ  TD  G E+++K ++ +   EYL+ TAP     L+    Q EN  +++  E
Sbjct: 406 IEFSQVVQKETDRLGLEMSAKQIYALLEAEYLQATAP---YTLKGHRLQEENGTSAVDVE 462

Query: 517 LIHNGKDVTVDGRGNGPLAAYANALEKLGIDVEIQEYNQHARTSGDDAEAAAYVLAEVNG 576
           +  +G+ V   G G GPL A   AL    + +EI +Y++H+  +G +A+AAAY+   ++G
Sbjct: 463 VAADGEVVHWRGIGKGPLEALVAALP---VKLEIMDYHEHSIGAGSNAKAAAYIEVRLDG 519

Query: 577 -RKVWGVGIAGSITYASLKAVTSAVNRAL 604
            R + G+GI  +IT AS++A+ SA+NRAL
Sbjct: 520 ERPLHGIGIDENITTASIRALFSAMNRAL 548


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: 909
Number of extensions: 36
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: 556
Length adjustment: 37
Effective length of query: 579
Effective length of database: 519
Effective search space:   300501
Effective search space used:   300501
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 GFF1244 Psest_1277 (2-isopropylmalate synthase, yeast type)
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.4779.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   7.2e-246  803.0   0.0   8.2e-246  802.8   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF1244  Psest_1277 2-isopropylmalate syn


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF1244  Psest_1277 2-isopropylmalate synthase, yeast type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  802.8   0.0  8.2e-246  8.2e-246       1     564 []       7     549 ..       7     549 .. 0.96

  Alignments for each domain:
  == domain 1  score: 802.8 bits;  conditional E-value: 8.2e-246
                           TIGR00970   1 pskkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkeievgfpsasqt 75 
                                         pskky+ f ai +++r+wp k it+ap wls dlrdGnq+li+pm++++k r+fk lv++G keievgfpsasqt
  lcl|FitnessBrowser__psRCH2:GFF1244   7 PSKKYRAFPAIDIPDRTWPSKTITQAPIWLSSDLRDGNQSLIEPMDAAKKMRFFKTLVQVGIKEIEVGFPSASQT 81 
                                         99************************************************************************* PP

                           TIGR00970  76 dfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdlfrevvfrasreevlalaveg 150
                                         dfdfvre+ie g ipddvtiqvltq+re+li rt+e+l+Gak+aivh+ynat++ fr++vf+++++ v+++av++
  lcl|FitnessBrowser__psRCH2:GFF1244  82 DFDFVRELIEGGHIPDDVTIQVLTQAREDLITRTFESLKGAKQAIVHYYNATAPSFRRIVFNQDKAGVVNIAVNA 156
                                         *************************************************************************** PP

                           TIGR00970 151 sklvrklvkdaaksketrwsfeyspesfsdtelefavevceavkeviepteerpiifnlpatvevatpnvyadsi 225
                                         ++++++l+   a+++et w+feyspe fs te+efavevc+av ev++pt+e+ +i+nlpatve atpn+yad+i
  lcl|FitnessBrowser__psRCH2:GFF1244 157 AQIIKRLA---AQNPETAWRFEYSPEIFSSTEPEFAVEVCNAVIEVFQPTPEQKLILNLPATVEAATPNIYADQI 228
                                         99998875...66789*********************************************************** PP

                           TIGR00970 226 eylstniaerekvilslhphndrGtavaaaelGllaGadrieGclfGnGertGnvdlvtlalnlytqGvspnldf 300
                                         e++++++  r++v++slh+hndrGt+vaa+elGl+aGadr+eGclfGnGertGnvdlvt+aln+ytqG++p+ldf
  lcl|FitnessBrowser__psRCH2:GFF1244 229 EWFCRHVDRRDSVLVSLHTHNDRGTGVAATELGLMAGADRVEGCLFGNGERTGNVDLVTVALNMYTQGIDPQLDF 303
                                         *************************************************************************** PP

                           TIGR00970 301 sdldeilrvvercnkipvherhpygGdlvvtafsGshqdaikkGldaldkkkaaadtlwkvpylpldpkdvgrey 375
                                         sd+d +++vve+cn++pvh+rhpy Gdlv+tafsGshqdai+kG+  +d      d +w+vpylp+dp d+gr y
  lcl|FitnessBrowser__psRCH2:GFF1244 304 SDIDAVRKVVEECNQLPVHPRHPYVGDLVHTAFSGSHQDAIRKGFSQQD-----PDSIWEVPYLPIDPADIGRSY 373
                                         *********************************************8765.....3789***************** PP

                           TIGR00970 376 eavirvnsqsGkGGvayvlktdlGldlprrlqiefssvvkdiadskGkelsskeisdlfkeeyllnveqlerisl 450
                                         eavirvnsqsGkGG++++l +++G++lprr+qiefs+vv++ +d  G e+s+k+i+ l++ eyl ++ ++  ++ 
  lcl|FitnessBrowser__psRCH2:GFF1244 374 EAVIRVNSQSGKGGITFLLEQEYGISLPRRMQIEFSQVVQKETDRLGLEMSAKQIYALLEAEYLQATAPY-TLKG 447
                                         ***************************************************************9965555.3444 PP

                           TIGR00970 451 vdyaveddGteskvitavvkikgekkdieGsGnGplsalvdaladllnvdvavadysehalgsGddakaasyvel 525
                                         +    e++G  + ++   v  +ge ++  G G Gpl alv al     v+++++dy eh++g+G++akaa+y+e+
  lcl|FitnessBrowser__psRCH2:GFF1244 448 HR-LQEENG--TSAVDVEVAADGEVVHWRGIGKGPLEALVAALP----VKLEIMDYHEHSIGAGSNAKAAAYIEV 515
                                         33.345566..88999*************************996....6679**********************9 PP

                           TIGR00970 526 svrrasdaekatvwGvGiaedvtsaslravlsavnraar 564
                                          +  +         G+Gi+e++t+as+ra++sa+nra r
  lcl|FitnessBrowser__psRCH2:GFF1244 516 RLDGER-----PLHGIGIDENITTASIRALFSAMNRALR 549
                                         998776.....589**********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (564 nodes)
Target sequences:                          1  (556 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: 10.27
//
[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