Alignments for a candidate for ilvI in Haloglycomyces albus DSM 45210

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Haloglycomyces albus DSM 45210

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_025274009.1 HALAL_RS0110735 acetolactate synthase large subunit

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_000527155.1:WP_025274009.1
          Length = 607

 Score =  813 bits (2101), Expect = 0.0
 Identities = 395/601 (65%), Positives = 471/601 (78%), Gaps = 7/601 (1%)

Query: 13  KPEPHSAANEPKHPAARPKHVALQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLF 72
           +P+P   A     P  R +       TGAQ V++SL +L V+ +FGIPGGA+LP YDPL 
Sbjct: 9   RPKPAKPA-----PPPRMRETVDPTFTGAQLVVKSLAQLDVEAVFGIPGGAILPTYDPLL 63

Query: 73  DSKKLRHVLVRHEQGAGHAASGYAHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVA 132
           DS  +RH+LVRHEQGAGHAA+GYA  TGRVGVCMATSGPGATNLVT LADA MDS+P+VA
Sbjct: 64  DSADVRHILVRHEQGAGHAATGYAAATGRVGVCMATSGPGATNLVTTLADAHMDSVPIVA 123

Query: 133 ITGQVGRGLIGTDAFQEADISGITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVL 192
           ITGQV    IG+DAFQEADI GITMPITKH++LV   DDIPR+LAEAFHIAA+GRPG VL
Sbjct: 124 ITGQVASNAIGSDAFQEADIHGITMPITKHSYLVEKVDDIPRILAEAFHIAATGRPGPVL 183

Query: 193 VDIPKDVLQGQCTFSWPPRMELPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRG 252
           VDIPKD+   +  F WPP M LPGY+P T+PHS+Q+REAA L+A + +PV+Y GGGVI+ 
Sbjct: 184 VDIPKDIQSAKTGFHWPPTMHLPGYRPVTQPHSKQIREAAALLAESNRPVIYAGGGVIKS 243

Query: 253 EATEQLRELAELTGIPVVTTLMARGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALG 312
           EA  +L  LA+ +G+PV TTLMARGAFPD H Q++GMPGMHGTV AV ALQ+SDL++ALG
Sbjct: 244 EAHAELLHLADRSGVPVTTTLMARGAFPDDHPQHVGMPGMHGTVPAVYALQKSDLIVALG 303

Query: 313 TRFDDRVTGKLDSFAPEAKVIHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHI 372
            RFDDRVTGKLD+FAP+AK++H DIDPAEIGKNR ADVPIVGD KA ++ +         
Sbjct: 304 ARFDDRVTGKLDAFAPDAKIVHVDIDPAEIGKNRTADVPIVGDCKAALSAITEAYEQQR- 362

Query: 373 PGTIEMADWWAYLNGVRKTYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQM 432
           P    +  WW  L+ +RK YP+ Y    + +L P+YVIE+LG +A  D ++ AGVGQHQM
Sbjct: 363 PDASRLLAWWDQLSDLRKRYPVGYDKSDETNLVPQYVIERLGALAPEDTIWTAGVGQHQM 422

Query: 433 WAAQFIRYEKPRSWLNSGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELAT 492
           WA+QFI Y +P+++LNSGGLGTMG+A+PAAMGAK+  P   VWAIDGDGCFQMTNQELAT
Sbjct: 423 WASQFISYNRPKTFLNSGGLGTMGYAVPAAMGAKLGYPDQCVWAIDGDGCFQMTNQELAT 482

Query: 493 CAVEGIPVKVALINNGNLGMVRQWQSLFYAERYSQTDLATH-SHRIPDFVKLAEALGCVG 551
           CA+EG+P+KVA+INNGNLGMVRQWQ+LFY +RYS TDL TH + RIPDFV LAEALGCVG
Sbjct: 483 CALEGLPIKVAVINNGNLGMVRQWQTLFYDQRYSNTDLGTHGAARIPDFVALAEALGCVG 542

Query: 552 LRCEREEDVVDVINQARAINDCPVVIDFIVGADAQVWPMVAAGTSNDEIQAARGIRPLFD 611
           LR E  E+V  VI QA AIND PVV+DF VG DA VWPMV AG SNDEI  AR +RP FD
Sbjct: 543 LRAETSEEVDSVIEQANAINDRPVVVDFTVGKDAMVWPMVPAGLSNDEILYARDLRPQFD 602

Query: 612 D 612
           +
Sbjct: 603 E 603


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: 1243
Number of extensions: 53
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: 607
Length adjustment: 37
Effective length of query: 581
Effective length of database: 570
Effective search space:   331170
Effective search space used:   331170
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_025274009.1 HALAL_RS0110735 (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.11759.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-236  771.4   0.1   2.9e-236  771.2   0.1    1.0  1  lcl|NCBI__GCF_000527155.1:WP_025274009.1  HALAL_RS0110735 acetolactate syn


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000527155.1:WP_025274009.1  HALAL_RS0110735 acetolactate synthase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  771.2   0.1  2.9e-236  2.9e-236       2     554 ..      30     592 ..      29     595 .. 0.97

  Alignments for each domain:
  == domain 1  score: 771.2 bits;  conditional E-value: 2.9e-236
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               +ga+++v+sl + +ve vfG+PGGa+lp yd l  + +++hilvrheq+a haa Gya a+G+vGv++a
  lcl|NCBI__GCF_000527155.1:WP_025274009.1  30 TGAQLVVKSLAQLDVEAVFGIPGGAILPTYDPLLdSADVRHILVRHEQGAGHAATGYAAATGRVGVCMA 98 
                                               79******************************997889******************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatnlvt +a+a++dsvP+v++tGqva+++iGsdafqe+di Git+p+tkhs+lv+k++d+p+il
  lcl|NCBI__GCF_000527155.1:WP_025274009.1  99 TSGPGATNLVTTLADAHMDSVPIVAITGQVASNAIGSDAFQEADIHGITMPITKHSYLVEKVDDIPRIL 167
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                                eaf+ia+tGrPGPvlvd+Pkd+++a++ ++ + +++lpgy+p +++h +qi++a+ l++++++Pv+++
  lcl|NCBI__GCF_000527155.1:WP_025274009.1 168 AEAFHIAATGRPGPVLVDIPKDIQSAKTGFHWPPTMHLPGYRPVTQPHSKQIREAAALLAESNRPVIYA 236
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgGvi++ea++el +la+r  +pvtttl+  Gafp+dhp+ +gm GmhGt  a +a++++dl++a+Gar
  lcl|NCBI__GCF_000527155.1:WP_025274009.1 237 GGGVIKSEAHAELLHLADRSGVPVTTTLMARGAFPDDHPQHVGMPGMHGTVPAVYALQKSDLIVALGAR 305
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkeke...Wlek 342
                                               fddrvtg+l+ fap+aki+h+didPaeigkn+++d+pivGd+k  l+ + ++ ++++ + ++   W+++
  lcl|NCBI__GCF_000527155.1:WP_025274009.1 306 FDDRVTGKLDAFAPDAKIVHVDIDPAEIGKNRTADVPIVGDCKAALSAITEAYEQQRPDASRllaWWDQ 374
                                               *****************************************************999544443347**** PP

                                 TIGR00118 343 ieewkkeyilkldeeees.ikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlG 410
                                               +++++k+y++ +d+++e+ + Pq+vi++l  l+++++i t++vGqhqmwa+qf ++++p++f++sgGlG
  lcl|NCBI__GCF_000527155.1:WP_025274009.1 375 LSDLRKRYPVGYDKSDETnLVPQYVIERLGALAPEDTIWTAGVGQHQMWASQFISYNRPKTFLNSGGLG 443
                                               ***********99987766************************************************** PP

                                 TIGR00118 411 tmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfye 479
                                               tmG+ +Paa+Gak++ p++ v a++Gdg fqm+ qel+t++  ++p+k+ ++nn  lGmv+qWq lfy+
  lcl|NCBI__GCF_000527155.1:WP_025274009.1 444 TMGYAVPAAMGAKLGYPDQCVWAIDGDGCFQMTNQELATCALEGLPIKVAVINNGNLGMVRQWQTLFYD 512
                                               ********************************************************************* PP

                                 TIGR00118 480 erysetklas....elpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPm 543
                                               +rys+t l++      pdfv+laea+G +g+r e+ ee+++ +++a + + +pv++d++v k++ v+Pm
  lcl|NCBI__GCF_000527155.1:WP_025274009.1 513 QRYSNTDLGThgaaRIPDFVALAEALGCVGLRAETSEEVDSVIEQANAINdRPVVVDFTVGKDAMVWPM 581
                                               *****98865222268******************************998879***************** PP

                                 TIGR00118 544 vapGagldelv 554
                                               v+ G ++de++
  lcl|NCBI__GCF_000527155.1:WP_025274009.1 582 VPAGLSNDEIL 592
                                               *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (607 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: 10.10
//
[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