Alignments for a candidate for ilvI in Enterococcus termitis LMG 8895

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Enterococcus termitis LMG 8895

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_069663720.1 BCR25_RS11370 biosynthetic-type acetolactate synthase large subunit

Query= metacyc::MONOMER-18810
         (585 letters)



>NCBI__GCF_001730305.1:WP_069663720.1
          Length = 564

 Score =  494 bits (1273), Expect = e-144
 Identities = 269/563 (47%), Positives = 364/563 (64%), Gaps = 16/563 (2%)

Query: 21  GAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYARAT 80
           G+ IL+ AL ++ V+ ++GYPGGAVL +YD L+      HIL RHEQ AVHAA+GYA+AT
Sbjct: 11  GSRILIDALLKQKVDMIFGYPGGAVLPLYDALY-DGDIPHILTRHEQGAVHAAEGYAKAT 69

Query: 81  GKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITRPI 140
           GK GV +VTSGPG TNA+TGIA A  DSIPM+V TG V T  IG+DAFQE D +G+T PI
Sbjct: 70  GKPGVVVVTSGPGATNALTGIADAMSDSIPMIVFTGQVVTDGIGKDAFQEADVIGLTMPI 129

Query: 141 VKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRSYNP 200
            K+N+ V+D ++L   I++AF IA TGR GPVV+D+PKD++      +    + + SY P
Sbjct: 130 TKNNYQVRDTKELPRIIEEAFHIATTGRKGPVVIDLPKDMTVMEAAADTEVKLHLPSYQP 189

Query: 201 VNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGLGAF 260
             K +  Q++K +  L  A++P +  G GV+ ANA  EL +       P  ++L+GLGA 
Sbjct: 190 TIKPNKLQVKKLMEALSVAKKPLVLVGAGVLHANAGKELVEFITKYQVPALSSLLGLGAV 249

Query: 261 PGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHIDID 320
           P   + F+GM GMHG++ ANMA+ +CD+LI IG+RFDDR+   P  F S A  I HIDID
Sbjct: 250 PTEQELFLGMGGMHGSFAANMALTDCDLLINIGSRFDDRLASAPKEFASNA-LIAHIDID 308

Query: 321 PSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKW--WEQIEQWRSV-DCL 377
           P+ I K ++ DIPIV + K+ L+E++    A DI     A  +W  W ++   R      
Sbjct: 309 PAEIGKIIETDIPIVADAKETLKEML----AIDI-----AGTEWSDWNKLNLTRKKRHPF 359

Query: 378 KYDRSSEI-IKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGT 436
            YD+  +  IKPQ V+E I ELT+G+A I +DVGQHQMWAAQFY F   ++ + SGGLGT
Sbjct: 360 HYDKEQQAEIKPQKVIEFIGELTQGEAIIATDVGQHQMWAAQFYPFKNEKQLVTSGGLGT 419

Query: 437 MGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVR 496
           MG G+P A+G K   P+KEVV   G+G  QM  QEL+   +Y+ P+KI  LNN  LGMVR
Sbjct: 420 MGYGVPAAIGAKLGCPDKEVVLFVGDGGFQMTNQELAILNEYNIPIKIVILNNQSLGMVR 479

Query: 497 QWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLD 556
           QWQE  ++ R S S   + PDFVK+AEAY   G+R++  + +E  L   F+ +   V ++
Sbjct: 480 QWQESFFNGRRSESVFSSQPDFVKMAEAYHIKGVRIDDPTTLENDLTTIFK-ETGPVLIE 538

Query: 557 FQTDPTENVWPMVQAGKGISEML 579
               PTE+V PMV AGK   +ML
Sbjct: 539 VMVSPTEHVLPMVPAGKANYQML 561


Lambda     K      H
   0.319    0.135    0.407 

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: 839
Number of extensions: 32
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: 585
Length of database: 564
Length adjustment: 36
Effective length of query: 549
Effective length of database: 528
Effective search space:   289872
Effective search space used:   289872
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_069663720.1 BCR25_RS11370 (biosynthetic-type acetolactate synthase large 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.1484345.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.8e-239  780.3   2.5   5.8e-239  780.1   2.5    1.0  1  NCBI__GCF_001730305.1:WP_069663720.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001730305.1:WP_069663720.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  780.1   2.5  5.8e-239  5.8e-239       2     556 ..      10     563 ..       9     564 .] 0.97

  Alignments for each domain:
  == domain 1  score: 780.1 bits;  conditional E-value: 5.8e-239
                             TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlatsGPG 74 
                                           +g++il+++l k++v+++fGyPGGavlp+ydalyd+++ hil+rheq+a+haa+Gya+a+Gk+Gvv++tsGPG
  NCBI__GCF_001730305.1:WP_069663720.1  10 SGSRILIDALLKQKVDMIFGYPGGAVLPLYDALYDGDIPHILTRHEQGAVHAAEGYAKATGKPGVVVVTSGPG 82 
                                           6899********************************************************************* PP

                             TIGR00118  75 atnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiast 147
                                           atn++tgia+a+ ds+P++v+tGqv t+ iG+dafqe+d++G+t+p+tk +++v+++++lp+i++eaf+ia+t
  NCBI__GCF_001730305.1:WP_069663720.1  83 ATNALTGIADAMSDSIPMIVFTGQVVTDGIGKDAFQEADVIGLTMPITKNNYQVRDTKELPRIIEEAFHIATT 155
                                           ************************************************************************* PP

                             TIGR00118 148 GrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseel 220
                                           Gr GPv++dlPkd+t  e   ++e k++lp+y+pt+k++klq+kk++e+++ akkP++lvG+Gv++a+a +el
  NCBI__GCF_001730305.1:WP_069663720.1 156 GRKGPVVIDLPKDMTVMEAAADTEVKLHLPSYQPTIKPNKLQVKKLMEALSVAKKPLVLVGAGVLHANAGKEL 228
                                           ************************************************************************* PP

                             TIGR00118 221 kelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeak 293
                                           +e+  + ++p  ++llGlGa+p +++l+lgm GmhG+ +an+a++++dlli +G rfddr ++  ++fa++a 
  NCBI__GCF_001730305.1:WP_069663720.1 229 VEFITKYQVPALSSLLGLGAVPTEQELFLGMGGMHGSFAANMALTDCDLLINIGSRFDDRLASAPKEFASNAL 301
                                           ************************************************************************* PP

                             TIGR00118 294 iihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeees.ikPqk 365
                                           i hididPaeigk++++dipiv dak+ l+e+l+   + ++ + +W +     kk++++++d+e+++ ikPqk
  NCBI__GCF_001730305.1:WP_069663720.1 302 IAHIDIDPAEIGKIIETDIPIVADAKETLKEMLAIDIAGTEWS-DWNKLNLTRKKRHPFHYDKEQQAeIKPQK 373
                                           *********************************9887764444.376666667778888998877666***** PP

                             TIGR00118 366 vikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdg 438
                                           vi+ + +l+++eai++tdvGqhqmwaaqfy++k+ ++ +tsgGlGtmG+G+Paa+Gak++ p+++vv  +Gdg
  NCBI__GCF_001730305.1:WP_069663720.1 374 VIEFIGELTQGEAIIATDVGQHQMWAAQFYPFKNEKQLVTSGGLGTMGYGVPAAIGAKLGCPDKEVVLFVGDG 446
                                           ************************************************************************* PP

                             TIGR00118 439 sfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekp 511
                                           +fqm+ qel+ + ey+ip+kivilnn+ lGmv+qWqe f+++r se+ ++s +pdfvk+aeay +kg+ri +p
  NCBI__GCF_001730305.1:WP_069663720.1 447 GFQMTNQELAILNEYNIPIKIVILNNQSLGMVRQWQESFFNGRRSESVFSS-QPDFVKMAEAYHIKGVRIDDP 518
                                           **************************************************5.********************* PP

                             TIGR00118 512 eeleeklkealeskepvlldvevdkeeevlPmvapGagldelvee 556
                                             le+ l+ ++++++pvl++v v  +e+vlPmv+ G+++ +++++
  NCBI__GCF_001730305.1:WP_069663720.1 519 TTLENDLTTIFKETGPVLIEVMVSPTEHVLPMVPAGKANYQMLGV 563
                                           ****************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (564 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 31.00
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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