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.21176.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: 00:00:00.04
# Mc/sec: 7.96
//
[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:

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:

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:

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:

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