Alignments for a candidate for ilvI in Desulfitobacterium hafniense DCB-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Desulfitobacterium hafniense DCB-2

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_015944692.1 DHAF_RS18025 acetolactate synthase, large subunit, biosynthetic type

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_000021925.1:WP_015944692.1
          Length = 563

 Score =  541 bits (1395), Expect = e-158
 Identities = 283/565 (50%), Positives = 383/565 (67%), Gaps = 8/565 (1%)

Query: 37  QLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASGYA 96
           +++GAQAVI  L++  V+++FG PGGAVL +YD L++++   H+L RHEQGA HAA GYA
Sbjct: 2   RMSGAQAVIECLKQENVEIVFGYPGGAVLTLYDALYETQ-FPHILTRHEQGAVHAADGYA 60

Query: 97  HVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGIT 156
             TG+VGVC+ATSGPGATNL+T +A A MDSIP+VAITGQV   LIG D+FQEAD++GIT
Sbjct: 61  RSTGKVGVCIATSGPGATNLITGIATAYMDSIPMVAITGQVAVSLIGRDSFQEADVTGIT 120

Query: 157 MPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRMELPG 216
            PITKHN+LV+   ++PRV  EAFHIA +GRPG VL+D+ KDV   +  F +P  + L G
Sbjct: 121 TPITKHNYLVKDVSELPRVFKEAFHIARTGRPGPVLIDVAKDVFAKELDFHYPDNVHLRG 180

Query: 217 YKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLMAR 276
           Y+P  +  ++ + + A+ ++ A++P+L+VGGGV   + +  LRE  E T IPV+++LM  
Sbjct: 181 YRPIFEGDAQIIAQVAEELSKAQRPLLFVGGGVNLADVSPALREFVEYTRIPVISSLMGL 240

Query: 277 GAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKVIHAD 336
           G  PD H QN GM GMHGT AA  A   +DLLI LG RFDDRVTG +  FA +AKVIH D
Sbjct: 241 GCIPDQHPQNYGMVGMHGTYAANMATTHADLLIGLGVRFDDRVTGLVADFASKAKVIHFD 300

Query: 337 IDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTI-EMADWWAYLNGVRKTYPLS 395
           IDPAE+ KN  A++ +VGD+K  I  L+  ++       +    +W   L+  R+  PL+
Sbjct: 301 IDPAEVNKNIIANIRVVGDLKWSIPALLNQVKERAAETWMGSNREWKKQLDEWREDNPLT 360

Query: 396 YGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGLGTM 455
           Y P+ +G + P+++I+++   A  DAV V  VGQHQMWA+QF  Y++PR+ L SGGLGTM
Sbjct: 361 YLPR-EGMIMPQHLIQRVSHFAAEDAVVVTDVGQHQMWASQFYEYKRPRTLLTSGGLGTM 419

Query: 456 GFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGMVRQ 515
           G+ +PAA+GA++  PG ++    GDG F M  QEL+T A   +PVKV ++NN  LGMV Q
Sbjct: 420 GYGLPAALGAQVGCPGRQIVCFSGDGGFMMNCQELSTLADLDLPVKVFILNNQVLGMVAQ 479

Query: 516 WQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQARAINDCPV 575
           WQ +FY   YS T L   +    DFVKLAEA+G  GLR    +DV   I +A AI   PV
Sbjct: 480 WQRMFYNGHYSHTTLKGRT----DFVKLAEAMGVTGLRVTEPQDVDMAIQKAFAIKG-PV 534

Query: 576 VIDFIVGADAQVWPMVAAGTSNDEI 600
           V++  + AD  V PMV AG   D++
Sbjct: 535 VVEIRIPADENVLPMVPAGGRLDQM 559


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: 942
Number of extensions: 43
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: 618
Length of database: 563
Length adjustment: 37
Effective length of query: 581
Effective length of database: 526
Effective search space:   305606
Effective search space used:   305606
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_015944692.1 DHAF_RS18025 (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.5372.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-246  805.4   0.6   1.5e-246  805.1   0.6    1.0  1  lcl|NCBI__GCF_000021925.1:WP_015944692.1  DHAF_RS18025 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021925.1:WP_015944692.1  DHAF_RS18025 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  805.1   0.6  1.5e-246  1.5e-246       1     554 [.       3     560 ..       3     562 .. 0.99

  Alignments for each domain:
  == domain 1  score: 805.1 bits;  conditional E-value: 1.5e-246
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               ++ga++++e lk+e+ve+vfGyPGGavl +ydaly+ ++ hil+rheq+a+haadGyar++GkvGv++a
  lcl|NCBI__GCF_000021925.1:WP_015944692.1   3 MSGAQAVIECLKQENVEIVFGYPGGAVLTLYDALYETQFPHILTRHEQGAVHAADGYARSTGKVGVCIA 71 
                                               79******************************************************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatnl+tgiatay+ds+P+v++tGqva sliG d+fqe+d++Git p+tkh++lvk++++lp+++
  lcl|NCBI__GCF_000021925.1:WP_015944692.1  72 TSGPGATNLITGIATAYMDSIPMVAITGQVAVSLIGRDSFQEADVTGITTPITKHNYLVKDVSELPRVF 140
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               keaf+ia tGrPGPvl+d+ kdv ++e++++++++v+l+gy+p  +g+ + i++++e ++ka++P+l+v
  lcl|NCBI__GCF_000021925.1:WP_015944692.1 141 KEAFHIARTGRPGPVLIDVAKDVFAKELDFHYPDNVHLRGYRPIFEGDAQIIAQVAEELSKAQRPLLFV 209
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgGv  a+ s  l+e++e ++ipv+++l+GlG++p++hp+  gm+GmhGt++an+a ++adlli++G+r
  lcl|NCBI__GCF_000021925.1:WP_015944692.1 210 GGGVNLADVSPALREFVEYTRIPVISSLMGLGCIPDQHPQNYGMVGMHGTYAANMATTHADLLIGLGVR 278
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee.....ekkekeWl 340
                                               fddrvtg +a fa++ak+ih+didPae++kn+ ++i +vGd k  +  ll+++ke+       +++eW+
  lcl|NCBI__GCF_000021925.1:WP_015944692.1 279 FDDRVTGLVADFASKAKVIHFDIDPAEVNKNIIANIRVVGDLKWSIPALLNQVKERaaetwMGSNREWK 347
                                               *********************************************9999999999876665556667** PP

                                 TIGR00118 341 ekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGl 409
                                               ++++ew+++++l++  +e+ i Pq++i+++s+++ ++a+v tdvGqhqmwa+qfy++k+pr+ +tsgGl
  lcl|NCBI__GCF_000021925.1:WP_015944692.1 348 KQLDEWREDNPLTYLPREGMIMPQHLIQRVSHFAAEDAVVVTDVGQHQMWASQFYEYKRPRTLLTSGGL 416
                                               ********************************************************************* PP

                                 TIGR00118 410 GtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfy 478
                                               GtmG+GlPaalGa+v+ p  ++v+ +Gdg+f+mn+qelst++++d+pvk+ ilnn++lGmv+qWq++fy
  lcl|NCBI__GCF_000021925.1:WP_015944692.1 417 GTMGYGLPAALGAQVGCPGRQIVCFSGDGGFMMNCQELSTLADLDLPVKVFILNNQVLGMVAQWQRMFY 485
                                               ********************************************************************* PP

                                 TIGR00118 479 eerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapG 547
                                               ++ ys+t+l+ + +dfvklaea+Gv+g+r+++p++++ ++++a++ k+pv++++++  +e+vlPmv+ G
  lcl|NCBI__GCF_000021925.1:WP_015944692.1 486 NGHYSHTTLK-GRTDFVKLAEAMGVTGLRVTEPQDVDMAIQKAFAIKGPVVVEIRIPADENVLPMVPAG 553
                                               **********.6********************************************************* PP

                                 TIGR00118 548 agldelv 554
                                               ++ld+++
  lcl|NCBI__GCF_000021925.1:WP_015944692.1 554 GRLDQMI 560
                                               *****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (563 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.96
//
[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