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_008807982.1 KVAR_RS24855 acetolactate synthase 2 catalytic subunit

Query= SwissProt::P0DP90
         (548 letters)



>NCBI__GCF_000025465.1:WP_008807982.1
          Length = 548

 Score =  995 bits (2572), Expect = 0.0
 Identities = 490/548 (89%), Positives = 519/548 (94%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARA 60
           MNGAQWVVHALR QGV+TVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARA
Sbjct: 1   MNGAQWVVHALRTQGVDTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARA 60

Query: 61  TGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLA 120
           TGKTGVCIATSGPGATNLITGLADALLDSIP+VAITGQV+APFIGTDAFQEVDVLGLSLA
Sbjct: 61  TGKTGVCIATSGPGATNLITGLADALLDSIPIVAITGQVAAPFIGTDAFQEVDVLGLSLA 120

Query: 121 CTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVT 180
           CTKHSFLVQSL+ELPR++AEAF VA SGRPGPVLVDIPKDIQ+A G+L+P F+TV++E+ 
Sbjct: 121 CTKHSFLVQSLDELPRVIAEAFQVANSGRPGPVLVDIPKDIQMAQGELDPHFSTVDDEMA 180

Query: 181 FPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEAD 240
           FP AEV QA QMLA++QKPMLYVGGGVGMAQAVPALREFLA T+MPATCTLKGLG V AD
Sbjct: 181 FPQAEVAQALQMLAQSQKPMLYVGGGVGMAQAVPALREFLAVTRMPATCTLKGLGVVAAD 240

Query: 241 YPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDPAEM 300
           YPYYLGMLGMHGTKAAN AVQECDLLIAVGARFDDRVTGKLNTFAPHA VIHMDIDPAE+
Sbjct: 241 YPYYLGMLGMHGTKAANLAVQECDLLIAVGARFDDRVTGKLNTFAPHAKVIHMDIDPAEL 300

Query: 301 NKLRQAHVALQGDLNALLPALQQPLNQYDWQQHCAQLRDEHSWRYDHPGDAIYAPLLLKQ 360
           NKLRQAH+ L GDLN LLPALQQPL    W++H A LR EH+WRYDHPG+AIYAPLLLKQ
Sbjct: 301 NKLRQAHIGLTGDLNRLLPALQQPLAIDAWREHNAALRTEHAWRYDHPGEAIYAPLLLKQ 360

Query: 361 LSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVGAQVARPND 420
           LSDRKPAD VVTTDVGQHQMW+AQH+ +TRPENFITSSGLGTMGFGLPAAVGAQVARP+D
Sbjct: 361 LSDRKPADSVVTTDVGQHQMWSAQHMTYTRPENFITSSGLGTMGFGLPAAVGAQVARPDD 420

Query: 421 TVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYSETTLTD 480
           TV+CISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYSETTLTD
Sbjct: 421 TVICISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYSETTLTD 480

Query: 481 NPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVWPLVPPGASN 540
           NPDFL LASAFGI GQHITRKDQVEAALDTML+S GPYLLHVSIDELENVWPLVPPGASN
Sbjct: 481 NPDFLTLASAFGIPGQHITRKDQVEAALDTMLSSQGPYLLHVSIDELENVWPLVPPGASN 540

Query: 541 SEMLEKLS 548
           +EMLEKLS
Sbjct: 541 AEMLEKLS 548


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: 1065
Number of extensions: 28
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: 548
Length of database: 548
Length adjustment: 36
Effective length of query: 512
Effective length of database: 512
Effective search space:   262144
Effective search space used:   262144
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_008807982.1 KVAR_RS24855 (acetolactate synthase 2 catalytic 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.14023.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-219  716.5   0.0   1.2e-219  716.3   0.0    1.0  1  lcl|NCBI__GCF_000025465.1:WP_008807982.1  KVAR_RS24855 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025465.1:WP_008807982.1  KVAR_RS24855 acetolactate synthase 2 catalytic subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  716.3   0.0  1.2e-219  1.2e-219       1     555 [.       1     545 [.       1     547 [. 0.97

  Alignments for each domain:
  == domain 1  score: 716.3 bits;  conditional E-value: 1.2e-219
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               ++ga+ +v++l+++gv+tvfGyPGGa++p+ydalyd+++eh+l rheq+aa aa Gyara+Gk+Gv++a
  lcl|NCBI__GCF_000025465.1:WP_008807982.1   1 MNGAQWVVHALRTQGVDTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARATGKTGVCIA 69 
                                               78******************************************************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatnl+tg+a+a lds+P+v++tGqva+  iG+dafqe+d+lG++l++tkhsflv++ ++lp+++
  lcl|NCBI__GCF_000025465.1:WP_008807982.1  70 TSGPGATNLITGLADALLDSIPIVAITGQVAAPFIGTDAFQEVDVLGLSLACTKHSFLVQSLDELPRVI 138
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                                eaf++a++GrPGPvlvd+Pkd++ a+ el+ +    + +   ++   ++ +++al+++++++kP+l+v
  lcl|NCBI__GCF_000025465.1:WP_008807982.1 139 AEAFQVANSGRPGPVLVDIPKDIQMAQGELDPH----FSTVDDEMAFPQAEVAQALQMLAQSQKPMLYV 203
                                               **************************9999887....555667777788899***************** PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgGv +a+a   l+e+   +++p t+tl GlG + +d p  lgmlGmhGtk+anlav+e+dlliavGar
  lcl|NCBI__GCF_000025465.1:WP_008807982.1 204 GGGVGMAQAVPALREFLAVTRMPATCTLKGLGVVAADYPYYLGMLGMHGTKAANLAVQECDLLIAVGAR 272
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekiee 345
                                               fddrvtg+l++fap+ak+ih+didPae++k ++++i + Gd ++ l  l + l      +  W e+ + 
  lcl|NCBI__GCF_000025465.1:WP_008807982.1 273 FDDRVTGKLNTFAPHAKVIHMDIDPAELNKLRQAHIGLTGDLNRLLPALQQPL----AID-AWREHNAA 336
                                               *****************************************776666555443....444.4******* PP

                                 TIGR00118 346 wkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGf 414
                                               +++e+  ++d+  e+i    ++k+ls   + +++vttdvGqhqmw+aq+ ++++p++fits+GlGtmGf
  lcl|NCBI__GCF_000025465.1:WP_008807982.1 337 LRTEHAWRYDHPGEAIYAPLLLKQLSDRKPADSVVTTDVGQHQMWSAQHMTYTRPENFITSSGLGTMGF 405
                                               *****************99************************************************** PP

                                 TIGR00118 415 GlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerys 483
                                               GlPaa+Ga+va p++tv++++Gdgsf+mn+qel t+++ ++p+kiv+l+n+ lGmv+qWq+lf++erys
  lcl|NCBI__GCF_000025465.1:WP_008807982.1 406 GLPAAVGAQVARPDDTVICISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYS 474
                                               ********************************************************************* PP

                                 TIGR00118 484 etklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGaglde 552
                                               et+l+ ++pdf  la a+G+ g++i++++++e++l+ +l+s++p+ll v++d+ e+v+P+v+pGa+++e
  lcl|NCBI__GCF_000025465.1:WP_008807982.1 475 ETTLT-DNPDFLTLASAFGIPGQHITRKDQVEAALDTMLSSQGPYLLHVSIDELENVWPLVPPGASNAE 542
                                               *****.6************************************************************** PP

                                 TIGR00118 553 lve 555
                                               ++e
  lcl|NCBI__GCF_000025465.1:WP_008807982.1 543 MLE 545
                                               *97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (548 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: 00:00:00.02
# Mc/sec: 12.20
//
[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