Alignments for a candidate for ilvI in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Klebsiella michiganensis M5al

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate BWI76_RS04695 BWI76_RS04695 acetolactate synthase 3 large subunit

Query= BRENDA::P00893
         (574 letters)



>FitnessBrowser__Koxy:BWI76_RS04695
          Length = 574

 Score = 1066 bits (2757), Expect = 0.0
 Identities = 525/574 (91%), Positives = 547/574 (95%)

Query: 1   MEMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADG 60
           MEMLSGAEMVV+SL+DQGVKQVFGYPGGAVLDIYDALHT+GGIDHVLVRHEQAAVHMADG
Sbjct: 1   MEMLSGAEMVVQSLVDQGVKQVFGYPGGAVLDIYDALHTLGGIDHVLVRHEQAAVHMADG 60

Query: 61  LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120
           LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLV+LSGQVATSLIGYDAFQECDMVG
Sbjct: 61  LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVILSGQVATSLIGYDAFQECDMVG 120

Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180
           ISRPVVKHSFLVKQTEDIP VLKKAFWLAASGRPGPVVVDLPKDILNPA KLPYVWP++V
Sbjct: 121 ISRPVVKHSFLVKQTEDIPGVLKKAFWLAASGRPGPVVVDLPKDILNPAKKLPYVWPDTV 180

Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240
           SMRSYNPTT+GHKGQIKRALQTLVAAKKPVVYVGGGAI A C  QL   VE L LPV  S
Sbjct: 181 SMRSYNPTTSGHKGQIKRALQTLVAAKKPVVYVGGGAINAQCEPQLYTLVEKLKLPVASS 240

Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300
           LMGLGAFPA+H+QALGMLGMHGTYEANMTMHN+DVIFAVGVRFDDRTTNNLA+YCPNATV
Sbjct: 241 LMGLGAFPASHQQALGMLGMHGTYEANMTMHNSDVIFAVGVRFDDRTTNNLARYCPNATV 300

Query: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWRAR 360
           LHIDIDPTSISKTV AD+PIVGDAR VLEQMLELL  E   QPLDEIRDWWQQIEQWRAR
Sbjct: 301 LHIDIDPTSISKTVPADVPIVGDARLVLEQMLELLEHEETQQPLDEIRDWWQQIEQWRAR 360

Query: 361 QCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSGGL 420
            CL+YDT S KIKPQAVIET+WRLT GDAYVTSDVGQHQMFAALYYPFDKPRRWINSGGL
Sbjct: 361 HCLQYDTQSGKIKPQAVIETIWRLTHGDAYVTSDVGQHQMFAALYYPFDKPRRWINSGGL 420

Query: 421 GTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYLGM 480
           GTMGFGLPAALGVKMALPEETV+CVTGDGSIQMNIQELSTALQYELPVLV+NLNNRYLGM
Sbjct: 421 GTMGFGLPAALGVKMALPEETVICVTGDGSIQMNIQELSTALQYELPVLVLNLNNRYLGM 480

Query: 481 VKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNNRL 540
           VKQWQDM+YSGRHSQSYM+SLPDF R+AEAYGHVGI+IS P ELE+KL+EALEQVRNNRL
Sbjct: 481 VKQWQDMLYSGRHSQSYMESLPDFARVAEAYGHVGIRISDPQELEAKLAEALEQVRNNRL 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: 1217
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 BWI76_RS04695 BWI76_RS04695 (acetolactate synthase 3 large subunit)
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.26556.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   6.7e-282  921.8   0.3   7.8e-282  921.6   0.3    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS04695  BWI76_RS04695 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS04695  BWI76_RS04695 acetolactate synthase 3 large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  921.6   0.3  7.8e-282  7.8e-282       1     556 [.       4     569 ..       4     570 .. 0.98

  Alignments for each domain:
  == domain 1  score: 921.6 bits;  conditional E-value: 7.8e-282
                               TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlat 70 
                                             l+gae++v+sl ++gv++vfGyPGGavl+iydal+  ++++h+lvrheqaa+h+adG+ara+G+vGvvl+t
  lcl|FitnessBrowser__Koxy:BWI76_RS04695   4 LSGAEMVVQSLVDQGVKQVFGYPGGAVLDIYDALHtLGGIDHVLVRHEQAAVHMADGLARATGEVGVVLVT 74 
                                             68*********************************99********************************** PP

                               TIGR00118  71 sGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkea 141
                                             sGPGatn++tgiatay+ds+Plv+l+GqvatsliG+dafqe+d++Gi++pv+khsflvk++ed+p +lk+a
  lcl|FitnessBrowser__Koxy:BWI76_RS04695  75 SGPGATNAITGIATAYMDSIPLVILSGQVATSLIGYDAFQECDMVGISRPVVKHSFLVKQTEDIPGVLKKA 145
                                             *********************************************************************** PP

                               TIGR00118 142 feiastGrPGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPvllvGgG 210
                                             f++a++GrPGPv+vdlPkd+ +++ +l++   ++v++++y+pt++ghk qik+al+++ +akkPv++vGgG
  lcl|FitnessBrowser__Koxy:BWI76_RS04695 146 FWLAASGRPGPVVVDLPKDILNPAKKLPYVwpDTVSMRSYNPTTSGHKGQIKRALQTLVAAKKPVVYVGGG 216
                                             ***************************999889************************************** PP

                               TIGR00118 211 viiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrv 281
                                             +i a+++ +l  l+e+lk+pv+++l+GlGafp+ h++algmlGmhGt+ean++++++d+++avG+rfddr+
  lcl|FitnessBrowser__Koxy:BWI76_RS04695 217 AINAQCEPQLYTLVEKLKLPVASSLMGLGAFPASHQQALGMLGMHGTYEANMTMHNSDVIFAVGVRFDDRT 287
                                             *********************************************************************** PP

                               TIGR00118 282 tgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wlekieewk 347
                                             t+nla+++p+a+++hididP++i+k+v +d+pivGda+ vle++l+ l++e      +e++ W+++ie+w+
  lcl|FitnessBrowser__Koxy:BWI76_RS04695 288 TNNLARYCPNATVLHIDIDPTSISKTVPADVPIVGDARLVLEQMLELLEHEetqqPLDEIRdWWQQIEQWR 358
                                             **********************************************9998855544456678********* PP

                               TIGR00118 348 keyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPa 418
                                             ++++l++d+++++ikPq+vi+++++l++++a+vt+dvGqhqm+aa +y+++kpr++i+sgGlGtmGfGlPa
  lcl|FitnessBrowser__Koxy:BWI76_RS04695 359 ARHCLQYDTQSGKIKPQAVIETIWRLTHGDAYVTSDVGQHQMFAALYYPFDKPRRWINSGGLGTMGFGLPA 429
                                             *********************************************************************** PP

                               TIGR00118 419 alGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklas 489
                                             alG+k+a peetv++vtGdgs+qmn+qelst+ +y++pv +++lnn++lGmvkqWq+++y++r+s+++++s
  lcl|FitnessBrowser__Koxy:BWI76_RS04695 430 ALGVKMALPEETVICVTGDGSIQMNIQELSTALQYELPVLVLNLNNRYLGMVKQWQDMLYSGRHSQSYMES 500
                                             **********************************************************************5 PP

                               TIGR00118 490 elpdfvklaeayGvkgiriekpeeleeklkealesk...epvlldvevdkeeevlPmvapGagldelvee 556
                                              lpdf+++aeayG++giri++p+ele+kl+eale+    ++v++dv+vd +e+v+Pm+++G+g+de++ +
  lcl|FitnessBrowser__Koxy:BWI76_RS04695 501 -LPDFARVAEAYGHVGIRISDPQELEAKLAEALEQVrnnRLVFVDVTVDGSEHVYPMQIRGGGMDEMWLS 569
                                             .******************************9987544599**************************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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 10.64
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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