Alignments for a candidate for ilvI in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Escherichia coli BW25113

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate 1936210 b0077 acetolactate synthase III large subunit (NCBI)

Query= BRENDA::P00893
         (574 letters)



>FitnessBrowser__Keio:1936210
          Length = 574

 Score = 1155 bits (2988), Expect = 0.0
 Identities = 574/574 (100%), Positives = 574/574 (100%)

Query: 1   MEMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADG 60
           MEMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADG
Sbjct: 1   MEMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADG 60

Query: 61  LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120
           LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG
Sbjct: 61  LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120

Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180
           ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV
Sbjct: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180

Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240
           SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS
Sbjct: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240

Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300
           LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV
Sbjct: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300

Query: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWRAR 360
           LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWRAR
Sbjct: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWRAR 360

Query: 361 QCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSGGL 420
           QCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSGGL
Sbjct: 361 QCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSGGL 420

Query: 421 GTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYLGM 480
           GTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYLGM
Sbjct: 421 GTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYLGM 480

Query: 481 VKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNNRL 540
           VKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNNRL
Sbjct: 481 VKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNNRL 540

Query: 541 VFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTERT 574
           VFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTERT
Sbjct: 541 VFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTERT 574


Lambda     K      H
   0.319    0.135    0.403 

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: 1272
Number of extensions: 31
Number of successful extensions: 1
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: 574
Length of database: 574
Length adjustment: 36
Effective length of query: 538
Effective length of database: 538
Effective search space:   289444
Effective search space used:   289444
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

Align candidate 1936210 b0077 (acetolactate synthase III large subunit (NCBI))
to HMM TIGR00118 (ilvB: acetolactate synthase, large subunit, biosynthetic type (EC 2.2.1.6))

# 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/TIGR00118.hmm
# target sequence database:        /tmp/gapView.8541.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00118  [M=557]
Accession:   TIGR00118
Description: acolac_lg: acetolactate synthase, large subunit, biosynthetic type
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     2e-289  946.7   1.1   2.3e-289  946.5   1.1    1.0  1  lcl|FitnessBrowser__Keio:1936210  b0077 acetolactate synthase III 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:1936210  b0077 acetolactate synthase III large subunit (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  946.5   1.1  2.3e-289  2.3e-289       1     556 [.       4     569 ..       4     570 .. 0.98

  Alignments for each domain:
  == domain 1  score: 946.5 bits;  conditional E-value: 2.3e-289
                         TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGat 76 
                                       l+gae++v+sl ++gv++vfGyPGGavl+iydal+  ++++h+lvrheqaa+h+adG+ara+G+vGvvl+tsGPGat
  lcl|FitnessBrowser__Keio:1936210   4 LSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHtVGGIDHVLVRHEQAAVHMADGLARATGEVGVVLVTSGPGAT 80 
                                       68*********************************99**************************************** PP

                         TIGR00118  77 nlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPv 153
                                       n++tgiatay+ds+Plvvl+GqvatsliG+dafqe+d++Gi++pv+khsflvk++ed+p++lk+af++a++GrPGPv
  lcl|FitnessBrowser__Keio:1936210  81 NAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVGISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPV 157
                                       ***************************************************************************** PP

                         TIGR00118 154 lvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlk 228
                                       +vdlPkd+ +++++l++   e+v++++y+pt++ghk qik+al+++ +akkPv++vGgG+i+a+++++lke++e+l+
  lcl|FitnessBrowser__Keio:1936210 158 VVDLPKDILNPANKLPYVwpESVSMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALN 234
                                       ****************9999********************************************************* PP

                         TIGR00118 229 ipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeig 305
                                       +pv+++l+GlGafp++h++algmlGmhGt+ean+++++ad+++avG+rfddr+t+nlak++p+a+++hididP++i+
  lcl|FitnessBrowser__Keio:1936210 235 LPVVCSLMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATVLHIDIDPTSIS 311
                                       ***************************************************************************** PP

                         TIGR00118 306 knvkvdipivGdakkvleellkklkee....ekkeke.WlekieewkkeyilkldeeeesikPqkvikelskllkde 377
                                       k+v++dipivGda++vle++l+ l++e      +e++ W+++ie+w+++++lk+d+++e+ikPq+vi++l++l+k++
  lcl|FitnessBrowser__Keio:1936210 312 KTVTADIPIVGDARQVLEQMLELLSQEsahqPLDEIRdWWQQIEQWRARQCLKYDTHSEKIKPQAVIETLWRLTKGD 388
                                       ***********************999966654456778*************************************** PP

                         TIGR00118 378 aivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveyd 454
                                       a+vt+dvGqhqm+aa +y+++kpr++i+sgGlGtmGfGlPaalG+k+a peetvv+vtGdgs+qmn+qelst+ +y+
  lcl|FitnessBrowser__Keio:1936210 389 AYVTSDVGQHQMFAALYYPFDKPRRWINSGGLGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYE 465
                                       ***************************************************************************** PP

                         TIGR00118 455 ipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk...epv 528
                                       +pv +v+lnn++lGmvkqWq+++y++r+s+++++s lpdfv+laeayG++gi+i++p+ele+kl+eale+    ++v
  lcl|FitnessBrowser__Keio:1936210 466 LPVLVVNLNNRYLGMVKQWQDMIYSGRHSQSYMQS-LPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVrnnRLV 541
                                       **********************************5.******************************9987544599* PP

                         TIGR00118 529 lldvevdkeeevlPmvapGagldelvee 556
                                       ++dv+vd +e+v+Pm+++G+g+de++ +
  lcl|FitnessBrowser__Keio:1936210 542 FVDVTVDGSEHVYPMQIRGGGMDEMWLS 569
                                       *************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (574 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 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 10.28
//
[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