Alignments for a candidate for ilvI in Clostridium kluyveri DSM 555

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Clostridium kluyveri DSM 555

Align acetohydroxy-acid synthase large subunit (EC 2.2.1.6) (characterized)
to candidate WP_012102013.1 CKL_RS07950 acetolactate synthase, large subunit, biosynthetic type

Query= metacyc::MONOMER-11900
         (599 letters)



>NCBI__GCF_000016505.1:WP_012102013.1
          Length = 536

 Score =  490 bits (1262), Expect = e-143
 Identities = 258/553 (46%), Positives = 354/553 (64%), Gaps = 22/553 (3%)

Query: 1   MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60
           M  AEA+I+ L+ E V ++FGYPG  ++P Y+A   SD+ H+L R EQ A H A GYARA
Sbjct: 1   MKVAEAVIQCLKQENVRMVFGYPGATVVPIYEAFRRSDIEHVLVRQEQGAGHCASGYARA 60

Query: 61  SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120
           +G+VGVC+ TSGPGATN++T +A A+ DS P+V +TGQV + LIG D FQE+D  G    
Sbjct: 61  TGEVGVCVVTSGPGATNVITAIAAAYMDSIPLVIITGQVKSVLIGKDVFQEVDITGATES 120

Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180
             K+NF ++    IP+  + AF IA TGR GPV ID+P D+ E ++D      P  V + 
Sbjct: 121 FTKYNFLVKDAKSIPKTIKEAFYIANTGRKGPVLIDIPTDIMEEDMDFQ---YPESVNIR 177

Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240
           GY PTT GH +QIKK +  + +++RPII  GGGV+L  A +EL + VE  +IPV  TLMG
Sbjct: 178 GYKPTTKGHFKQIKKVVDRLKTSERPIICVGGGVILGKAEKELKQFVEKCHIPVIHTLMG 237

Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHI 300
           KG + EN    +G++G HG   AN     SDVLI IG R SDR T  +K+FA  A IIHI
Sbjct: 238 KGSMDENSEYYVGLIGTHGFAYANKAAENSDVLILIGARASDRTTFGVKTFAKKADIIHI 297

Query: 301 DIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNSLK 360
           DIDPAEIGKN++  +PIVGD   I+ ++ K++  I  K     N  + I +W EN+  ++
Sbjct: 298 DIDPAEIGKNLDTYIPIVGDCANIIADLTKEITPIETK-----NWLDEIKEWKENLKVVR 352

Query: 361 KSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPRS 420
           K +  V         P+ ++K    V+ D+ + ++ I+T DVGQNQ+W A  FK    R 
Sbjct: 353 KPTDKV--------NPKYVLK----VVSDM-VEEDAILTADVGQNQLWCARNFKITGDRK 399

Query: 421 FLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVICIF 480
            L+SGGLGTMG+  P+AIGAK+A PD +VI   GDGGF M+  ELGT+ E N+ ++I +F
Sbjct: 400 LLTSGGLGTMGYSLPAAIGAKLACPDKRVIAFAGDGGFQMSVFELGTVTEKNVNLIIVVF 459

Query: 481 DNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEAIN 540
           +N  LGMV + QN      +  VNF   PDFIKL+E+YG+ A+R+ + NE  E  KEA+N
Sbjct: 460 NNSGLGMVREIQN-NRSLDEFGVNFRTNPDFIKLSEAYGLLAKRVANDNEFEEVFKEALN 518

Query: 541 CDEPYLLDFAIDP 553
            D  +L++  +DP
Sbjct: 519 SDRAFLIECIVDP 531


Lambda     K      H
   0.319    0.137    0.405 

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: 850
Number of extensions: 45
Number of successful extensions: 4
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: 599
Length of database: 536
Length adjustment: 36
Effective length of query: 563
Effective length of database: 500
Effective search space:   281500
Effective search space used:   281500
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_012102013.1 CKL_RS07950 (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.1297.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-207  675.8   1.5   2.6e-207  675.6   1.5    1.0  1  lcl|NCBI__GCF_000016505.1:WP_012102013.1  CKL_RS07950 acetolactate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016505.1:WP_012102013.1  CKL_RS07950 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  675.6   1.5  2.6e-207  2.6e-207       1     539 [.       1     534 [.       1     536 [] 0.98

  Alignments for each domain:
  == domain 1  score: 675.6 bits;  conditional E-value: 2.6e-207
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               +k ae++++ lk+e+v +vfGyPG +v+piy+a+  s++eh+lvr eq+a h a Gyara+G+vGv+++
  lcl|NCBI__GCF_000016505.1:WP_012102013.1   1 MKVAEAVIQCLKQENVRMVFGYPGATVVPIYEAFRRSDIEHVLVRQEQGAGHCASGYARATGEVGVCVV 69 
                                               6889***************************************************************** PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatn++t+ia ay+ds+Plv++tGqv++ liG+d fqe+di+G t + tk++flvk+a+ +p+++
  lcl|NCBI__GCF_000016505.1:WP_012102013.1  70 TSGPGATNVITAIAAAYMDSIPLVIITGQVKSVLIGKDVFQEVDITGATESFTKYNFLVKDAKSIPKTI 138
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               keaf+ia+tGr GPvl+d+P d++e++++++++e+v+++gykpt+kgh +qikk+++ ++++++P++ v
  lcl|NCBI__GCF_000016505.1:WP_012102013.1 139 KEAFYIANTGRKGPVLIDIPTDIMEEDMDFQYPESVNIRGYKPTTKGHFKQIKKVVDRLKTSERPIICV 207
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgGvi ++a++elk+++e+++ipv++tl+G+G+++e+ +  +g++G hG ++an a +++d+li +Gar
  lcl|NCBI__GCF_000016505.1:WP_012102013.1 208 GGGVILGKAEKELKQFVEKCHIPVIHTLMGKGSMDENSEYYVGLIGTHGFAYANKAAENSDVLILIGAR 276
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekiee 345
                                                +dr+t  +++fa++a iihididPaeigkn+ + ipivGd+ +++++l k+++  e+k+  Wl++i+e
  lcl|NCBI__GCF_000016505.1:WP_012102013.1 277 ASDRTTFGVKTFAKKADIIHIDIDPAEIGKNLDTYIPIVGDCANIIADLTKEITPIETKN--WLDEIKE 343
                                               ******************************************************999988..******* PP

                                 TIGR00118 346 wkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGf 414
                                               wk++    + +  ++++P++v+k +s +++++ai+t+dvGq+q+w a+ +k++  rk +tsgGlGtmG+
  lcl|NCBI__GCF_000016505.1:WP_012102013.1 344 WKENLK-VVRKPTDKVNPKYVLKVVSDMVEEDAILTADVGQNQLWCARNFKITGDRKLLTSGGLGTMGY 411
                                               **9876.67888899****************************************************** PP

                                 TIGR00118 415 GlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerys 483
                                                lPaa+Gak+a p++ v+a +Gdg+fqm++ el t++e +++++iv++nn+ lGmv+  q+    + + 
  lcl|NCBI__GCF_000016505.1:WP_012102013.1 412 SLPAAIGAKLACPDKRVIAFAGDGGFQMSVFELGTVTEKNVNLIIVVFNNSGLGMVREIQNNRSLDEFG 480
                                               ************************************************************987766665 PP

                                 TIGR00118 484 etklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeee 539
                                                 ++   +pdf+kl+eayG+ + r+++++e ee +keal+s++  l++  vd +e+
  lcl|NCBI__GCF_000016505.1:WP_012102013.1 481 V-NFR-TNPDFIKLSEAYGLLAKRVANDNEFEEVFKEALNSDRAFLIECIVDPHER 534
                                               4.455.37*******************************************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (536 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.05
//
[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