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_012102441.1 CKL_RS10305 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000016505.1:WP_012102441.1
          Length = 569

 Score =  399 bits (1025), Expect = e-115
 Identities = 240/564 (42%), Positives = 336/564 (59%), Gaps = 31/564 (5%)

Query: 1   MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLL-TRHEQAAAHAADGYAR 59
           +N ++ +   L+  K +++F YPGG + P  DA+     I L+ TR++QAA+  AD YAR
Sbjct: 2   INISKMIANKLKENKCKVIFEYPGGNVAPILDAVKLDGTIDLVVTRNDQAASLMADAYAR 61

Query: 60  ASGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPT------KLIGNDAFQEID 113
            +G+VGVC+ T GPGATNLVTG+A A+ DS P+VA+TGQV T      K      FQE+D
Sbjct: 62  VTGEVGVCMATVGPGATNLVTGIANAYFDSIPLVAITGQVGTGSLKGIKKTRQIGFQEVD 121

Query: 114 ALGLFMPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPI 173
            + +  PI K +  I K   + ++   AF IA+ GRPGPV ID+P DVQ   L   K  I
Sbjct: 122 IVNIVKPITKWSCMITKPEDVNQVIDEAFRIAREGRPGPVLIDIPMDVQRSMLQ--KLDI 179

Query: 174 PSKVKLIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIP 233
            ++V +I     +I   ++I   I+ I  + +P+I+AGGGV+L  A  EL  L E   IP
Sbjct: 180 LNRVDII--EKRSIVEQKKINLLIQKINLSSKPVIIAGGGVILGNAENELKVLAEKSQIP 237

Query: 234 VCTTLMGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITG-DIKSFA 292
           V  TLMG G    N  LALG +G +G++  N  L+E+D++I++G RF  R  G +I  F 
Sbjct: 238 VANTLMGLGSFDLNSKLALGFMGCYGSRACNKILAEADLIIALGNRFDVRAIGTEINKFQ 297

Query: 293 TNAKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQW 352
               IIH+D+D AEI   V  ++ I GD K +LK +I +L+ I N D+K+         W
Sbjct: 298 EGKFIIHVDVDKAEINNTVKTNLAINGDVKEVLKLIIDRLNEI-NIDTKK---------W 347

Query: 353 IENVNSLKKSSIPVMDY----DDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMW 408
           ++ ++ LK       +Y    +   ++PQ I+KE+  +      N   IIT+DVGQNQMW
Sbjct: 348 LDYISELKYKFNLDREYRLSDEYDKVRPQYIIKEISNLT-----NGKAIITSDVGQNQMW 402

Query: 409 MAHYFKTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTI 468
            A ++K +  R+ L+SGGLG MG+G P+AI AK AK D++VI ITGDG F MN QELGT 
Sbjct: 403 TAQFYKYRYTRTNLTSGGLGNMGYGLPAAIAAKYAKKDAQVINITGDGSFQMNMQELGTA 462

Query: 469 AEYNIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESP 528
             YN+PV I I  N TLG+V Q+Q+  +  +  S      PDFIKLAE YGIK  RI   
Sbjct: 463 VAYNLPVKIFILKNNTLGLVKQFQDKTFLGKATSTVIKYNPDFIKLAEVYGIKGLRISKA 522

Query: 529 NEINEALKEAINCDEPYLLDFAID 552
           +EI   +KEA+N D   +++  ID
Sbjct: 523 SEIKGIVKEALNYDGTVIVECYID 546


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: 831
Number of extensions: 43
Number of successful extensions: 7
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: 569
Length adjustment: 36
Effective length of query: 563
Effective length of database: 533
Effective search space:   300079
Effective search space used:   300079
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_012102441.1 CKL_RS10305 (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.22461.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-185  603.5   4.8   2.1e-185  603.3   4.8    1.0  1  lcl|NCBI__GCF_000016505.1:WP_012102441.1  CKL_RS10305 acetolactate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016505.1:WP_012102441.1  CKL_RS10305 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  603.3   4.8  2.1e-185  2.1e-185       4     551 ..       5     562 ..       2     566 .. 0.94

  Alignments for each domain:
  == domain 1  score: 603.3 bits;  conditional E-value: 2.1e-185
                                 TIGR00118   4 aeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlats 71 
                                               ++++ + lk+++ +++f yPGG v pi da+  d+ ++ +++r +qaa+ +ad yar++G+vGv++at 
  lcl|NCBI__GCF_000016505.1:WP_012102441.1   5 SKMIANKLKENKCKVIFEYPGGNVAPILDAVKlDGTIDLVVTRNDQAASLMADAYARVTGEVGVCMATV 73 
                                               6899****************************999********************************** PP

                                 TIGR00118  72 GPGatnlvtgiatayldsvPlvvltGqvat.sliGsd.....afqeidilGitlpvtkhsflvkkaedl 134
                                               GPGatnlvtgia+ay ds+Plv++tGqv t sl G        fqe+di+ i +p+tk+s +++k+ed+
  lcl|NCBI__GCF_000016505.1:WP_012102441.1  74 GPGATNLVTGIANAYFDSIPLVAITGQVGTgSLKGIKktrqiGFQEVDIVNIVKPITKWSCMITKPEDV 142
                                               ****************************984455643222337************************** PP

                                 TIGR00118 135 peilkeafeiastGrPGPvlvdlPkdvteaeie.leveekvelpgykptvkghklqikkaleliekakk 202
                                                +++ eaf ia  GrPGPvl+d+P dv+++ ++ l++ ++v++   +  v+  +++i+ +++ i+ + k
  lcl|NCBI__GCF_000016505.1:WP_012102441.1 143 NQVIDEAFRIAREGRPGPVLIDIPMDVQRSMLQkLDILNRVDIIEKRSIVE--QKKINLLIQKINLSSK 209
                                               ****************************99876156669999988777665..6789************ PP

                                 TIGR00118 203 PvllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlli 271
                                               Pv+++GgGvi ++a++elk lae+ +ipv+ tl+GlG+f+ + +lalg++G +G+++ n  + eadl+i
  lcl|NCBI__GCF_000016505.1:WP_012102441.1 210 PVIIAGGGVILGNAENELKVLAEKSQIPVANTLMGLGSFDLNSKLALGFMGCYGSRACNKILAEADLII 278
                                               ********************************************************************* PP

                                 TIGR00118 272 avGarfddrvtg.nlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeW 339
                                               a+G rfd r  g +++kf +   iih+d+d aei+ +vk++++i Gd+k+vl+ ++++l+e + ++k+W
  lcl|NCBI__GCF_000016505.1:WP_012102441.1 279 ALGNRFDVRAIGtEINKFQEGKFIIHVDVDKAEINNTVKTNLAINGDVKEVLKLIIDRLNEINIDTKKW 347
                                               *********87648*****9999********************************************** PP

                                 TIGR00118 340 lekieewkkeyilk....ldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfi 404
                                               l+ i+e+k +  l     l+ e ++++Pq++ike+s+l++++ai+t+dvGq+qmw+aqfyk++++r+ +
  lcl|NCBI__GCF_000016505.1:WP_012102441.1 348 LDYISELKYKFNLDreyrLSDEYDKVRPQYIIKEISNLTNGKAIITSDVGQNQMWTAQFYKYRYTRTNL 416
                                               *****99887654322227788899******************************************** PP

                                 TIGR00118 405 tsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473
                                               tsgGlG mG+GlPaa+ ak ak++++v+++tGdgsfqmn+qel t+v y++pvki il+n++lG+vkq+
  lcl|NCBI__GCF_000016505.1:WP_012102441.1 417 TSGGLGNMGYGLPAAIAAKYAKKDAQVINITGDGSFQMNMQELGTAVAYNLPVKIFILKNNTLGLVKQF 485
                                               ********************************************************************* PP

                                 TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlP 542
                                               q+  + ++ ++t ++  +pdf+klae yG+kg+ri+k +e++  +keal+ ++ v+++  +d++e ++P
  lcl|NCBI__GCF_000016505.1:WP_012102441.1 486 QDKTFLGKATSTVIKY-NPDFIKLAEVYGIKGLRISKASEIKGIVKEALNYDGTVIVECYIDSNELAIP 553
                                               ***9999999999995.9*************************************************** PP

                                 TIGR00118 543 mvapGagld 551
                                                +  G+ +d
  lcl|NCBI__GCF_000016505.1:WP_012102441.1 554 EIEGGHYID 562
                                               999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (569 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: 12.12
//
[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