Alignments for a candidate for ilvI in Klebsiella variicola At-22

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Klebsiella variicola At-22

Align Acetolactate synthase isozyme 2 large subunit; AHAS-II; ALS-II; Acetohydroxy-acid synthase II large subunit; EC 2.2.1.6 (characterized)
to candidate WP_012540267.1 KVAR_RS00135 acetolactate synthase, large subunit, biosynthetic type

Query= SwissProt::P0DP90
         (548 letters)



>NCBI__GCF_000025465.1:WP_012540267.1
          Length = 562

 Score =  500 bits (1288), Expect = e-146
 Identities = 262/550 (47%), Positives = 356/550 (64%), Gaps = 12/550 (2%)

Query: 3   GAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGG-VEHLLCRHEQGAAMAAIGYARAT 61
           GAQ VVH L  QG+  V G PGG+I+P+YDAL     + H+L RHEQGA   A G AR  
Sbjct: 15  GAQLVVHLLERQGITMVSGIPGGSILPIYDALSQSTQIRHILARHEQGAGFIAQGMARTE 74

Query: 62  GKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLAC 121
           GK  VC+A SGPGATNLIT +ADA LDSIP+V ITGQV A  IGTDAFQEVD  G+S+  
Sbjct: 75  GKPAVCMACSGPGATNLITAIADARLDSIPLVCITGQVPASMIGTDAFQEVDTYGISIPI 134

Query: 122 TKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVT- 180
           TKH++LV+ + ELP+++++AF +A SGRPGPV +DIPKD+Q A+ +LE      E     
Sbjct: 135 TKHNYLVRDIAELPQVISDAFRIAQSGRPGPVWIDIPKDVQAATIELETLPEPGERAPAP 194

Query: 181 -FPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEA 239
            F    V +A  M+  A++P+LY+GGGV    A   +R+      +P T TL  LG +  
Sbjct: 195 AFTPESVREAAAMINAAKRPVLYLGGGV--INAPQPIRDLAEKANLPTTMTLMALGMLPK 252

Query: 240 DYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDPAE 299
            +P  LGMLGMHG ++ NF +QE DLLI +GARFDDR  GK   F P+A +IH+DID +E
Sbjct: 253 AHPLSLGMLGMHGARSTNFILQEADLLIVLGARFDDRAIGKTEQFCPNAKIIHVDIDRSE 312

Query: 300 MNKLRQAHVALQGD----LNALLPALQ-QPLNQYDWQQHCAQLRDEHSWRYDHPGDAIYA 354
           + K++Q HVA+QGD    L  L+P ++ QP ++  W+Q  A L+ E         D +  
Sbjct: 313 LGKIKQPHVAIQGDVAEVLAQLIPQIEAQPRDE--WRQLVADLQREFPCAIPQESDPLSH 370

Query: 355 PLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVGAQ 414
             L+  ++     + ++TTDVGQHQMW AQ     RP  ++TS GLGTMGFGLPAA+GA 
Sbjct: 371 YGLINAVAACVDDEAIITTDVGQHQMWTAQAYPLNRPRQWLTSGGLGTMGFGLPAAIGAA 430

Query: 415 VARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYS 474
           +A P   V+C SGDGS MMN+QE+ T    QL +KI+LL+N+ LG+V Q Q LF+Q+   
Sbjct: 431 LANPQRKVICFSGDGSLMMNIQEMATAAENQLDVKIILLNNEALGLVHQQQSLFYQQGVF 490

Query: 475 ETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVWPLV 534
             T     +F+ +A+ FG+    +  +   +AAL  +++  GP L+HV ID  + V+P+V
Sbjct: 491 AATYPGMINFMQIAAGFGLQTCDLNNEADPQAALQAIIDRPGPALIHVRIDAQQKVYPMV 550

Query: 535 PPGASNSEML 544
           PPGA+N+EM+
Sbjct: 551 PPGAANTEMV 560


Lambda     K      H
   0.320    0.135    0.410 

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: 830
Number of extensions: 30
Number of successful extensions: 5
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: 548
Length of database: 562
Length adjustment: 36
Effective length of query: 512
Effective length of database: 526
Effective search space:   269312
Effective search space used:   269312
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 WP_012540267.1 KVAR_RS00135 (acetolactate synthase, large subunit, biosynthetic type)
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.31482.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-206  673.1   0.2   1.7e-206  672.9   0.2    1.0  1  lcl|NCBI__GCF_000025465.1:WP_012540267.1  KVAR_RS00135 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025465.1:WP_012540267.1  KVAR_RS00135 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  672.9   0.2  1.7e-206  1.7e-206       2     555 ..      14     561 ..      13     562 .] 0.97

  Alignments for each domain:
  == domain 1  score: 672.9 bits;  conditional E-value: 1.7e-206
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               +ga+++v+ l+++g+ +v G+PGG++lpiydal  + +++hil+rheq+a  +a+G+ar+ Gk+ v++a
  lcl|NCBI__GCF_000025465.1:WP_012540267.1  14 TGAQLVVHLLERQGITMVSGIPGGSILPIYDALSqSTQIRHILARHEQGAGFIAQGMARTEGKPAVCMA 82 
                                               79*******************************97889******************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                                sGPGatnl+t+ia+a lds+Plv +tGqv++s+iG+dafqe+d  Gi++p+tkh++lv++ ++lp+++
  lcl|NCBI__GCF_000025465.1:WP_012540267.1  83 CSGPGATNLITAIADARLDSIPLVCITGQVPASMIGTDAFQEVDTYGISIPITKHNYLVRDIAELPQVI 151
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                                +af ia++GrPGPv +d+Pkdv++a+iele+  +   ++  p     +  +++a+ +i++ak+Pvl+ 
  lcl|NCBI__GCF_000025465.1:WP_012540267.1 152 SDAFRIAQSGRPGPVWIDIPKDVQAATIELETLPEPGERA--PAPAFTPESVREAAAMINAAKRPVLYL 218
                                               ****************************999885544444..4455567789***************** PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgGvi  +a++ +++lae++++p t+tl+ lG +p+ hpl+lgmlGmhG++ +n+ ++eadlli +Gar
  lcl|NCBI__GCF_000025465.1:WP_012540267.1 219 GGGVI--NAPQPIRDLAEKANLPTTMTLMALGMLPKAHPLSLGMLGMHGARSTNFILQEADLLIVLGAR 285
                                               ****9..57899********************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekiee 345
                                               fddr  g+ ++f+p+akiih+did +e+gk+ + +++i Gd+ +vl++l+ +++++ ++e  W + +++
  lcl|NCBI__GCF_000025465.1:WP_012540267.1 286 FDDRAIGKTEQFCPNAKIIHVDIDRSELGKIKQPHVAIQGDVAEVLAQLIPQIEAQPRDE--WRQLVAD 352
                                               ******************************************************999998..******* PP

                                 TIGR00118 346 wkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGf 414
                                               +++e + ++ +e++++    +i+++   ++deai+ttdvGqhqmw+aq y+ ++pr+++tsgGlGtmGf
  lcl|NCBI__GCF_000025465.1:WP_012540267.1 353 LQREFPCAIPQESDPLSHYGLINAVAACVDDEAIITTDVGQHQMWTAQAYPLNRPRQWLTSGGLGTMGF 421
                                               ********************************************************************* PP

                                 TIGR00118 415 GlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerys 483
                                               GlPaa+Ga +a+p+ +v++ +Gdgs++mn+qe++t++e +++vki++lnne lG+v+q q+lfy++   
  lcl|NCBI__GCF_000025465.1:WP_012540267.1 422 GLPAAIGAALANPQRKVICFSGDGSLMMNIQEMATAAENQLDVKIILLNNEALGLVHQQQSLFYQQGVF 490
                                               *****************************************************************9998 PP

                                 TIGR00118 484 etklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGaglde 552
                                               +++   ++ +f+++a ++G+++  ++++++ +++l+ ++   +p+l+ v++d +++v+Pmv+pGa+++e
  lcl|NCBI__GCF_000025465.1:WP_012540267.1 491 AATYP-GMINFMQIAAGFGLQTCDLNNEADPQAALQAIIDRPGPALIHVRIDAQQKVYPMVPPGAANTE 558
                                               88887.59************************************************************* PP

                                 TIGR00118 553 lve 555
                                               +v+
  lcl|NCBI__GCF_000025465.1:WP_012540267.1 559 MVG 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: 00:00:00.04
# Mc/sec: 7.45
//
[ok]

This GapMind analysis is from Apr 10 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