Alignments for a candidate for ilvI in Thermomonospora curvata DSM 43183

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Thermomonospora curvata DSM 43183

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_012853873.1 TCUR_RS17515 acetolactate synthase large subunit

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_000024385.1:WP_012853873.1
          Length = 581

 Score =  852 bits (2200), Expect = 0.0
 Identities = 413/578 (71%), Positives = 484/578 (83%), Gaps = 3/578 (0%)

Query: 36  QQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASGY 95
           +Q+TGAQA+IR+LE +GVD +FGIPGGA+LP YDPLFDS K+RH+LVRHEQGAGHAA GY
Sbjct: 4   EQMTGAQALIRALENVGVDTVFGIPGGAILPAYDPLFDSTKVRHILVRHEQGAGHAAQGY 63

Query: 96  AHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGI 155
           A VTG+VGVCMATSGPGATNLVTP++DA MDS+P+VAITGQV  G IGTDAFQEADI GI
Sbjct: 64  AMVTGKVGVCMATSGPGATNLVTPISDAYMDSVPIVAITGQVTSGAIGTDAFQEADIVGI 123

Query: 156 TMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRMELP 215
           TMPITKHNFLV+   DI R + EAFHIA++GRPG VLVDI KD LQ    F+WP    LP
Sbjct: 124 TMPITKHNFLVKDPHDIARTIVEAFHIASTGRPGPVLVDIAKDALQATFDFTWPESPHLP 183

Query: 216 GYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLMA 275
           GY+P T+PH++QVREAA+L+  A++PVLYVGGGV++  A  +L+ LAELTG PVVTTLMA
Sbjct: 184 GYRPVTRPHAKQVREAARLLMEAKRPVLYVGGGVLKAGAAAELKVLAELTGAPVVTTLMA 243

Query: 276 RGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKVIHA 335
           +GA PDSH  ++GMPGMHGTVAAV ALQR+DLL+ALG RFDDRVTGKLDSFAPEAKV+HA
Sbjct: 244 KGALPDSHPLHVGMPGMHGTVAAVGALQRADLLVALGARFDDRVTGKLDSFAPEAKVVHA 303

Query: 336 DIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTI-EMADWWAYLNGVRKTYPL 394
           DIDPAEI KNRHADVPIVGD + VI +LI  ++  H  G   + A WW  L   ++TYPL
Sbjct: 304 DIDPAEISKNRHADVPIVGDAREVIADLIVAVQAEHEAGRRGDYAAWWKQLRAWQETYPL 363

Query: 395 SYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGLGT 454
            Y    DGSL+P+YVIE++G+IAGPDA +VAGVGQHQMWAAQFI+YE+P ++LNSGG GT
Sbjct: 364 GYDHPEDGSLAPQYVIEQIGKIAGPDAYYVAGVGQHQMWAAQFIKYERPGAFLNSGGAGT 423

Query: 455 MGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGMVR 514
           MG+AIPAAMGAK+A P   VWAIDGDGCFQMTNQELATCAVEGIP+KVA+INNGNLGMVR
Sbjct: 424 MGYAIPAAMGAKVAKPDATVWAIDGDGCFQMTNQELATCAVEGIPIKVAIINNGNLGMVR 483

Query: 515 QWQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQARAINDCP 574
           QWQ+LFY ERYS T+L  HS RIPDFVKLAEA GCVG+RC+R EDV + I +A  IND P
Sbjct: 484 QWQTLFYNERYSNTNL--HSKRIPDFVKLAEAYGCVGMRCDRAEDVEETIRKAMEINDTP 541

Query: 575 VVIDFIVGADAQVWPMVAAGTSNDEIQAARGIRPLFDD 612
           VVIDF+V  DA VWPMVAAGTSND+I+ AR + P +++
Sbjct: 542 VVIDFVVHQDAMVWPMVAAGTSNDDIKIARDLAPEWEN 579


Lambda     K      H
   0.319    0.136    0.414 

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: 1224
Number of extensions: 56
Number of successful extensions: 3
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: 618
Length of database: 581
Length adjustment: 37
Effective length of query: 581
Effective length of database: 544
Effective search space:   316064
Effective search space used:   316064
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_012853873.1 TCUR_RS17515 (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.7368.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-238  778.4   2.8   2.2e-238  778.2   2.8    1.0  1  lcl|NCBI__GCF_000024385.1:WP_012853873.1  TCUR_RS17515 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024385.1:WP_012853873.1  TCUR_RS17515 acetolactate synthase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  778.2   2.8  2.2e-238  2.2e-238       1     553 [.       6     567 ..       6     571 .. 0.98

  Alignments for each domain:
  == domain 1  score: 778.2 bits;  conditional E-value: 2.2e-238
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               ++ga++l+++l++ gv+tvfG+PGGa+lp yd l+ + +++hilvrheq+a haa+Gya ++GkvGv++
  lcl|NCBI__GCF_000024385.1:WP_012853873.1   6 MTGAQALIRALENVGVDTVFGIPGGAILPAYDPLFdSTKVRHILVRHEQGAGHAAQGYAMVTGKVGVCM 74 
                                               79*********************************7889****************************** PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               atsGPGatnlvt+i +ay+dsvP+v++tGqv++ +iG+dafqe+di+Git+p+tkh+flvk+++d++++
  lcl|NCBI__GCF_000024385.1:WP_012853873.1  75 ATSGPGATNLVTPISDAYMDSVPIVAITGQVTSGAIGTDAFQEADIVGITMPITKHNFLVKDPHDIART 143
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206
                                               + eaf+iastGrPGPvlvd+ kd  +a+++++ +e+ +lpgy+p +++h +q+++a+ l+++ak+Pvl+
  lcl|NCBI__GCF_000024385.1:WP_012853873.1 144 IVEAFHIASTGRPGPVLVDIAKDALQATFDFTWPESPHLPGYRPVTRPHAKQVREAARLLMEAKRPVLY 212
                                               ********************************************************************* PP

                                 TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275
                                               vGgGv++a+a +elk lae + +pv+ttl+ +Ga+p+ hpl +gm GmhGt +a  a++ adll+a+Ga
  lcl|NCBI__GCF_000024385.1:WP_012853873.1 213 VGGGVLKAGAAAELKVLAELTGAPVVTTLMAKGALPDSHPLHVGMPGMHGTVAAVGALQRADLLVALGA 281
                                               ********************************************************************* PP

                                 TIGR00118 276 rfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.W 339
                                               rfddrvtg+l++fapeak++h didPaei+kn+++d+pivGda++v+++l+ ++++e    ++ +   W
  lcl|NCBI__GCF_000024385.1:WP_012853873.1 282 RFDDRVTGKLDSFAPEAKVVHADIDPAEISKNRHADVPIVGDAREVIADLIVAVQAEheagRRGDYAaW 350
                                               ***************************************************99998866665556667* PP

                                 TIGR00118 340 lekieewkkeyilkldeeees.ikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsg 407
                                               +++++ w+++y+l +d+ e+  ++Pq+vi+++ k++  +a++ ++vGqhqmwaaqf k+++p  f++sg
  lcl|NCBI__GCF_000024385.1:WP_012853873.1 351 WKQLRAWQETYPLGYDHPEDGsLAPQYVIEQIGKIAGPDAYYVAGVGQHQMWAAQFIKYERPGAFLNSG 419
                                               ***************9977655*********************************************** PP

                                 TIGR00118 408 GlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqel 476
                                               G+GtmG+ +Paa+Gakvakp++tv a++Gdg fqm+ qel+t++  +ip+k+ i+nn  lGmv+qWq l
  lcl|NCBI__GCF_000024385.1:WP_012853873.1 420 GAGTMGYAIPAAMGAKVAKPDATVWAIDGDGCFQMTNQELATCAVEGIPIKVAIINNGNLGMVRQWQTL 488
                                               ********************************************************************* PP

                                 TIGR00118 477 fyeerysetklas.elpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPm 543
                                               fy+erys+t+l+s   pdfvklaeayG +g+r  + e++ee +++a+e + +pv++d++v++++ v+Pm
  lcl|NCBI__GCF_000024385.1:WP_012853873.1 489 FYNERYSNTNLHSkRIPDFVKLAEAYGCVGMRCDRAEDVEETIRKAMEINdTPVVIDFVVHQDAMVWPM 557
                                               **********986257********************************9879***************** PP

                                 TIGR00118 544 vapGagldel 553
                                               va G+++d++
  lcl|NCBI__GCF_000024385.1:WP_012853873.1 558 VAAGTSNDDI 567
                                               ******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (581 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: 00:00:00.03
# Mc/sec: 8.88
//
[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