Aligments for a candidate for ilvH in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Aligments for a candidate for ilvH in Escherichia coli BW25113

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate 17731 b3671 acetolactate synthase large subunit (NCBI)

Query= BRENDA::P08142
         (562 letters)



>FitnessBrowser__Keio:17731
          Length = 562

 Score = 1119 bits (2894), Expect = 0.0
 Identities = 562/562 (100%), Positives = 562/562 (100%)

Query: 1   MASSGTTSTRKRFTGAEFIVHFLEQQGIKIVTGIPGGSILPVYDALSQSTQIRHILARHE 60
           MASSGTTSTRKRFTGAEFIVHFLEQQGIKIVTGIPGGSILPVYDALSQSTQIRHILARHE
Sbjct: 1   MASSGTTSTRKRFTGAEFIVHFLEQQGIKIVTGIPGGSILPVYDALSQSTQIRHILARHE 60

Query: 61  QGAGFIAQGMARTDGKPAVCMACSGPGATNLVTAIADARLDSIPLICITGQVPASMIGTD 120
           QGAGFIAQGMARTDGKPAVCMACSGPGATNLVTAIADARLDSIPLICITGQVPASMIGTD
Sbjct: 61  QGAGFIAQGMARTDGKPAVCMACSGPGATNLVTAIADARLDSIPLICITGQVPASMIGTD 120

Query: 121 AFQEVDTYGISIPITKHNYLVRHIEELPQVMSDAFRIAQSGRPGPVWIDIPKDVQTAVFE 180
           AFQEVDTYGISIPITKHNYLVRHIEELPQVMSDAFRIAQSGRPGPVWIDIPKDVQTAVFE
Sbjct: 121 AFQEVDTYGISIPITKHNYLVRHIEELPQVMSDAFRIAQSGRPGPVWIDIPKDVQTAVFE 180

Query: 181 IETQPAMAEKAAAPAFSEESIRDAAAMINAAKRPVLYLGGGVINAPARVRELAEKAQLPT 240
           IETQPAMAEKAAAPAFSEESIRDAAAMINAAKRPVLYLGGGVINAPARVRELAEKAQLPT
Sbjct: 181 IETQPAMAEKAAAPAFSEESIRDAAAMINAAKRPVLYLGGGVINAPARVRELAEKAQLPT 240

Query: 241 TMTLMALGMLPKAHPLSLGMLGMHGVRSTNYILQEADLLIVLGARFDDRAIGKTEQFCPN 300
           TMTLMALGMLPKAHPLSLGMLGMHGVRSTNYILQEADLLIVLGARFDDRAIGKTEQFCPN
Sbjct: 241 TMTLMALGMLPKAHPLSLGMLGMHGVRSTNYILQEADLLIVLGARFDDRAIGKTEQFCPN 300

Query: 301 AKIIHVDIDRAELGKIKQPHVAIQADVDDVLAQLIPLVEAQPRAEWHQLVADLQREFPCP 360
           AKIIHVDIDRAELGKIKQPHVAIQADVDDVLAQLIPLVEAQPRAEWHQLVADLQREFPCP
Sbjct: 301 AKIIHVDIDRAELGKIKQPHVAIQADVDDVLAQLIPLVEAQPRAEWHQLVADLQREFPCP 360

Query: 361 IPKACDPLSHYGLINAVAACVDDNAIITTDVGQHQMWTAQAYPLNRPRQWLTSGGLGTMG 420
           IPKACDPLSHYGLINAVAACVDDNAIITTDVGQHQMWTAQAYPLNRPRQWLTSGGLGTMG
Sbjct: 361 IPKACDPLSHYGLINAVAACVDDNAIITTDVGQHQMWTAQAYPLNRPRQWLTSGGLGTMG 420

Query: 421 FGLPAAIGAALANPDRKVLCFSGDGSLMMNIQEMATASENQLDVKIILMNNEALGLVHQQ 480
           FGLPAAIGAALANPDRKVLCFSGDGSLMMNIQEMATASENQLDVKIILMNNEALGLVHQQ
Sbjct: 421 FGLPAAIGAALANPDRKVLCFSGDGSLMMNIQEMATASENQLDVKIILMNNEALGLVHQQ 480

Query: 481 QSLFYEQGVFAATYPGKINFMQIAAGFGLETCDLNNEADPQASLQEIINRPGPALIHVRI 540
           QSLFYEQGVFAATYPGKINFMQIAAGFGLETCDLNNEADPQASLQEIINRPGPALIHVRI
Sbjct: 481 QSLFYEQGVFAATYPGKINFMQIAAGFGLETCDLNNEADPQASLQEIINRPGPALIHVRI 540

Query: 541 DAEEKVYPMVPPGAANTEMVGE 562
           DAEEKVYPMVPPGAANTEMVGE
Sbjct: 541 DAEEKVYPMVPPGAANTEMVGE 562


Lambda     K      H
   0.320    0.135    0.400 

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: 1212
Number of extensions: 19
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: 562
Length of database: 562
Length adjustment: 36
Effective length of query: 526
Effective length of database: 526
Effective search space:   276676
Effective search space used:   276676
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 17731 b3671 (acetolactate synthase 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.7413.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   8.1e-206  670.7   0.4   9.2e-206  670.5   0.4    1.0  1  lcl|FitnessBrowser__Keio:17731  b3671 acetolactate synthase larg


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17731  b3671 acetolactate synthase large subunit (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  670.5   0.4  9.2e-206  9.2e-206       2     555 ..      14     561 ..      13     562 .] 0.98

  Alignments for each domain:
  == domain 1  score: 670.5 bits;  conditional E-value: 9.2e-206
                       TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGatnlv 79 
                                     +gae +v+ l+++g+++v G+PGG++lp+ydal  + +++hil+rheq+a  +a+G+ar+ Gk+ v++a sGPGatnlv
  lcl|FitnessBrowser__Keio:17731  14 TGAEFIVHFLEQQGIKIVTGIPGGSILPVYDALSqSTQIRHILARHEQGAGFIAQGMARTDGKPAVCMACSGPGATNLV 92 
                                     79*******************************97889***************************************** PP

                       TIGR00118  80 tgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPvlvdlP 158
                                     t+ia+a lds+Pl+ +tGqv++s+iG+dafqe+d  Gi++p+tkh++lv++ e+lp+++ +af ia++GrPGPv +d+P
  lcl|FitnessBrowser__Keio:17731  93 TAIADARLDSIPLICITGQVPASMIGTDAFQEVDTYGISIPITKHNYLVRHIEELPQVMSDAFRIAQSGRPGPVWIDIP 171
                                     ******************************************************************************* PP

                       TIGR00118 159 kdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlkipvtttllG 237
                                     kdv++a +e+e++  +  ++ +p    ++  i+ a+ +i++ak+Pvl+ GgGvi a  +++++elae++++p t+tl+ 
  lcl|FitnessBrowser__Keio:17731 172 KDVQTAVFEIETQPAMAEKAAAPAF--SEESIRDAAAMINAAKRPVLYLGGGVINA--PARVRELAEKAQLPTTMTLMA 246
                                     ********99999888777777766..5678***********************65..6789***************** PP

                       TIGR00118 238 lGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigknvkvdipivG 316
                                     lG +p+ hpl+lgmlGmhG + +n+ ++eadlli +Garfddr  g+ ++f+p+akiih+did ae+gk+ + +++i  
  lcl|FitnessBrowser__Keio:17731 247 LGMLPKAHPLSLGMLGMHGVRSTNYILQEADLLIVLGARFDDRAIGKTEQFCPNAKIIHVDIDRAELGKIKQPHVAIQA 325
                                     ******************************************************************************* PP

                       TIGR00118 317 dakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfy 395
                                     d+  vl++l+  ++++ + e  W + ++++++e +  + +  +++    +i+++   ++d+ai+ttdvGqhqmw+aq y
  lcl|FitnessBrowser__Keio:17731 326 DVDDVLAQLIPLVEAQPRAE--WHQLVADLQREFPCPIPKACDPLSHYGLINAVAACVDDNAIITTDVGQHQMWTAQAY 402
                                     **************999999..********************************************************* PP

                       TIGR00118 396 ktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWq 474
                                     + ++pr+++tsgGlGtmGfGlPaa+Ga +a+p+ +v++ +Gdgs++mn+qe++t++e +++vki+++nne lG+v+q q
  lcl|FitnessBrowser__Keio:17731 403 PLNRPRQWLTSGGLGTMGFGLPAAIGAALANPDRKVLCFSGDGSLMMNIQEMATASENQLDVKIILMNNEALGLVHQQQ 481
                                     ******************************************************************************* PP

                       TIGR00118 475 elfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldel 553
                                     +lfye+   +++   ++ +f+++a ++G+++  ++++++ ++ l+e+++  +p+l+ v++d ee+v+Pmv+pGa+++e+
  lcl|FitnessBrowser__Keio:17731 482 SLFYEQGVFAATYP-GKINFMQIAAGFGLETCDLNNEADPQASLQEIINRPGPALIHVRIDAEEKVYPMVPPGAANTEM 559
                                     *****998887777.58************************************************************** PP

                       TIGR00118 554 ve 555
                                     v+
  lcl|FitnessBrowser__Keio:17731 560 VG 561
                                     96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (562 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: 7.90
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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