Alignments for a candidate for ilvI in Desulfacinum hydrothermale DSM 13146

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Desulfacinum hydrothermale DSM 13146

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_084057655.1 B9A12_RS09535 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_900176285.1:WP_084057655.1
          Length = 572

 Score =  626 bits (1615), Expect = 0.0
 Identities = 323/570 (56%), Positives = 401/570 (70%), Gaps = 13/570 (2%)

Query: 21  GAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYARAT 80
           GA+I    L  E VE ++G+PGGAV+ +Y E+ K     HILVRHEQ A H ADGYARAT
Sbjct: 5   GAQIFFECLKRENVEVIFGFPGGAVIDLYHEMPKHD-IRHILVRHEQGAAHMADGYARAT 63

Query: 81  GKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITRPI 140
           GKVGV LVTSGPG TN VTGIATAY+DS+PMVV TG VPT  IG DAFQE D VGITRP 
Sbjct: 64  GKVGVCLVTSGPGATNTVTGIATAYMDSVPMVVFTGQVPTALIGNDAFQEVDIVGITRPC 123

Query: 141 VKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRSYNP 200
            KHN+LVKDVRDLA  I++AF++A TGRPGPV+VD+PKDV + +  + YPK + +  Y P
Sbjct: 124 TKHNYLVKDVRDLARVIREAFYLARTGRPGPVLVDLPKDVIQASTDFRYPKRVQLPGYRP 183

Query: 201 VNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGLGAF 260
             + H+GQI +A  LL+ A+RP IY GGGV+ ++A  EL +LA     PVT TLMGLG F
Sbjct: 184 TVEPHAGQINRAWDLLRKAKRPVIYAGGGVISSSAHRELTRLAEALQAPVTTTLMGLGGF 243

Query: 261 PGTSKQ----------FVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQ 310
           P   +           ++GMLGMHGT+ ANMA+QNCDVL A+GARFDDRV G  + F  +
Sbjct: 244 PAVVRNDKGQRELHPLWLGMLGMHGTFRANMAVQNCDVLFAVGARFDDRVTGKISGFAPK 303

Query: 311 ARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQ 370
           A KIIHID+DP+SISK V VDIPIVG+ K  L++L    K   ++   +  A W EQI Q
Sbjct: 304 A-KIIHIDVDPTSISKNVVVDIPIVGDCKAALRKLNDIAKQEPLENVDDLRAPWLEQIHQ 362

Query: 371 WRSVDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWIN 430
           WR    L Y +    IKPQYVVEKI+EL   +  I ++VGQ+QMWAAQ+Y F +PR  + 
Sbjct: 363 WRETYPLAYKKEGNGIKPQYVVEKIFELADEETIITTEVGQNQMWAAQYYHFAKPRTLLT 422

Query: 431 SGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNG 490
           SGGLGTMG GLP A+G + AFP++ V+ + G+GSIQM IQEL T +  + PVK+  LNN 
Sbjct: 423 SGGLGTMGYGLPAAIGAQAAFPDRLVIDVAGDGSIQMNIQELITAVCNELPVKVAILNNR 482

Query: 491 YLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKD 550
           YLGMVRQWQE+ YD  +  + +DA PDFV+LAEAYG VG+R +   +VEP LREA  ++ 
Sbjct: 483 YLGMVRQWQELFYDKNFCATCLDASPDFVRLAEAYGAVGLRAKSMEEVEPVLREALSVQ- 541

Query: 551 RTVFLDFQTDPTENVWPMVQAGKGISEMLL 580
           + V +DF   P E V+PMV AGK ISEMLL
Sbjct: 542 KPVLMDFWVSPEEGVYPMVPAGKNISEMLL 571


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: 937
Number of extensions: 30
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: 572
Length adjustment: 36
Effective length of query: 549
Effective length of database: 536
Effective search space:   294264
Effective search space used:   294264
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_084057655.1 B9A12_RS09535 (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.12145.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-262  857.2   0.0   2.9e-262  857.0   0.0    1.0  1  lcl|NCBI__GCF_900176285.1:WP_084057655.1  B9A12_RS09535 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900176285.1:WP_084057655.1  B9A12_RS09535 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  857.0   0.0  2.9e-262  2.9e-262       2     554 ..       4     570 ..       3     572 .] 0.97

  Alignments for each domain:
  == domain 1  score: 857.0 bits;  conditional E-value: 2.9e-262
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlat 70 
                                               +ga+i+ e lk+e+ve++fG+PGGav+++y ++ + +++hilvrheq+aah+adGyara+GkvGv+l+t
  lcl|NCBI__GCF_900176285.1:WP_084057655.1   4 TGAQIFFECLKRENVEVIFGFPGGAVIDLYHEMPKHDIRHILVRHEQGAAHMADGYARATGKVGVCLVT 72 
                                               79******************************************************************* PP

                                 TIGR00118  71 sGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilk 139
                                               sGPGatn+vtgiatay+dsvP+vv+tGqv+t+liG+dafqe+di+Git+p+tkh++lvk+++dl+++++
  lcl|NCBI__GCF_900176285.1:WP_084057655.1  73 SGPGATNTVTGIATAYMDSVPMVVFTGQVPTALIGNDAFQEVDIVGITRPCTKHNYLVKDVRDLARVIR 141
                                               ********************************************************************* PP

                                 TIGR00118 140 eafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvG 208
                                               eaf++a tGrPGPvlvdlPkdv +a+++++++++v+lpgy+ptv++h  qi++a +l++kak+Pv+++G
  lcl|NCBI__GCF_900176285.1:WP_084057655.1 142 EAFYLARTGRPGPVLVDLPKDVIQASTDFRYPKRVQLPGYRPTVEPHAGQINRAWDLLRKAKRPVIYAG 210
                                               ********************************************************************* PP

                                 TIGR00118 209 gGviiaeaseelkelaerlkipvtttllGlGafp..........edhplalgmlGmhGtkeanlavsea 267
                                               gGvi + a++el++lae+l++pvtttl+GlG+fp          e hpl lgmlGmhGt  an+av+++
  lcl|NCBI__GCF_900176285.1:WP_084057655.1 211 GGVISSSAHRELTRLAEALQAPVTTTLMGLGGFPavvrndkgqrELHPLWLGMLGMHGTFRANMAVQNC 279
                                               *********************************9444433333335999******************** PP

                                 TIGR00118 268 dlliavGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee...e 333
                                               d+l+avGarfddrvtg+++ fap+akiihid+dP++i+knv vdipivGd+k  l++l + +k+e   +
  lcl|NCBI__GCF_900176285.1:WP_084057655.1 280 DVLFAVGARFDDRVTGKISGFAPKAKIIHIDVDPTSISKNVVVDIPIVGDCKAALRKLNDIAKQEpleN 348
                                               **********************************************************99888887765 PP

                                 TIGR00118 334 kkeke..WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkp 400
                                                ++ +  Wle+i++w+++y+l++++e + ikPq+v++++ +l+++e+i+tt+vGq+qmwaaq+y++ kp
  lcl|NCBI__GCF_900176285.1:WP_084057655.1 349 VDDLRapWLEQIHQWRETYPLAYKKEGNGIKPQYVVEKIFELADEETIITTEVGQNQMWAAQYYHFAKP 417
                                               5566668************************************************************** PP

                                 TIGR00118 401 rkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGm 469
                                               r+ +tsgGlGtmG+GlPaa+Ga+ a p+  v++v+Gdgs+qmn+qel t+v  ++pvk+ ilnn++lGm
  lcl|NCBI__GCF_900176285.1:WP_084057655.1 418 RTLLTSGGLGTMGYGLPAAIGAQAAFPDRLVIDVAGDGSIQMNIQELITAVCNELPVKVAILNNRYLGM 486
                                               ********************************************************************* PP

                                 TIGR00118 470 vkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkee 538
                                               v+qWqelfy++ + +t+l + +pdfv+laeayG++g+r ++ ee+e  l+eal++++pvl+d+ v  ee
  lcl|NCBI__GCF_900176285.1:WP_084057655.1 487 VRQWQELFYDKNFCATCLDA-SPDFVRLAEAYGAVGLRAKSMEEVEPVLREALSVQKPVLMDFWVSPEE 554
                                               *******************5.************************************************ PP

                                 TIGR00118 539 evlPmvapGagldelv 554
                                                v+Pmv+ G++++e++
  lcl|NCBI__GCF_900176285.1:WP_084057655.1 555 GVYPMVPAGKNISEML 570
                                               **************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (572 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: 12.75
//
[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