Alignments for a candidate for ilvI in Methanothermobacter thermautotrophicus Delta H

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Methanothermobacter thermautotrophicus Delta H

Align acetohydroxy-acid synthase large subunit (EC 2.2.1.6) (characterized)
to candidate WP_048061055.1 MTH_RS06905 acetolactate synthase, large subunit, biosynthetic type

Query= metacyc::MONOMER-11900
         (599 letters)



>NCBI__GCF_000008645.1:WP_048061055.1
          Length = 574

 Score =  689 bits (1777), Expect = 0.0
 Identities = 334/572 (58%), Positives = 426/572 (74%), Gaps = 23/572 (4%)

Query: 1   MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60
           M G +A+I++L  +  + +FGYPGG LLP YD L+ S+L H+L RHEQ AAHAADGYARA
Sbjct: 1   MKGGQAIIRSLLDQGADTVFGYPGGQLLPLYDMLYDSELKHILVRHEQCAAHAADGYARA 60

Query: 61  SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120
           SG+VGVCI TSGPGATNLVTG+ATA+ DS+P+VA+ GQVPT LIGNDAFQE+D +G+ MP
Sbjct: 61  SGRVGVCIATSGPGATNLVTGIATAYMDSAPIVAIAGQVPTHLIGNDAFQEVDMIGITMP 120

Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELEL--DIDKHPIPSKVK 178
           I KH+FQ     +IP I R++F IA+TGRPGPV IDLPKD+QE E+  ++D   +P    
Sbjct: 121 ITKHSFQPSDASEIPAIVRASFHIAKTGRPGPVVIDLPKDIQEQEIMEEVDDLELP---- 176

Query: 179 LIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTL 238
             GY P   GHP QIK+A +LI  +++P+ILAGGGV++SGA+ E+ +L +L+  PV TTL
Sbjct: 177 --GYRPNVKGHPLQIKRAAELIRRSEKPVILAGGGVIISGASREIKELSDLIKAPVTTTL 234

Query: 239 MGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKII 298
           +GKG   E+HP A+GM+GMHG K AN  + E D LI++GCRFSDR TG++  FA NA+II
Sbjct: 235 LGKGSFPEDHPSAMGMLGMHGRKVANLTVDECDCLIAVGCRFSDRTTGNVAEFAPNARII 294

Query: 299 HIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNS 358
           H+DIDPAEIGKNV VDVPIVGDA+ +L+E+I +L     +DS          QW+E+V  
Sbjct: 295 HVDIDPAEIGKNVGVDVPIVGDARNVLRELIAKLKKYEKRDS----------QWLESVQK 344

Query: 359 LKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTP 418
            +   +P M YD++P+KPQ+++KE+  V+DD      T++TTDVGQNQMWMAH++ ++ P
Sbjct: 345 FRADCMPRMSYDEVPLKPQQVIKEISQVLDD-----ETVVTTDVGQNQMWMAHFYTSRAP 399

Query: 419 RSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVIC 478
           R F+SSGGLGTMGFGFP+AIGAKVA PDS V+ + GDGGF+M CQ+L TI EY+IPVVIC
Sbjct: 400 RKFISSGGLGTMGFGFPAAIGAKVALPDSDVVAVCGDGGFLMVCQDLATIREYDIPVVIC 459

Query: 479 IFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEA 538
           I DNR LGMV QWQ LFY +R    + G  PDF+KLAES+G++A RIE P E +EAL  A
Sbjct: 460 IMDNRHLGMVAQWQRLFYDERMSHTHLGEVPDFVKLAESFGVEAERIEEPGETSEALSRA 519

Query: 539 INCDEPYLLDFAIDPSSALSMVPPGAKLTNII 570
           I   EP LLD  IDP   L MVPPG  LT I+
Sbjct: 520 IRSGEPALLDIVIDPDEILPMVPPGCGLTEIV 551


Lambda     K      H
   0.319    0.137    0.405 

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: 968
Number of extensions: 36
Number of successful extensions: 4
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: 599
Length of database: 574
Length adjustment: 37
Effective length of query: 562
Effective length of database: 537
Effective search space:   301794
Effective search space used:   301794
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_048061055.1 MTH_RS06905 (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.12970.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.5e-290  948.8   0.0   5.2e-290  948.6   0.0    1.0  1  lcl|NCBI__GCF_000008645.1:WP_048061055.1  MTH_RS06905 acetolactate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008645.1:WP_048061055.1  MTH_RS06905 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  948.6   0.0  5.2e-290  5.2e-290       1     556 [.       1     553 [.       1     554 [. 0.99

  Alignments for each domain:
  == domain 1  score: 948.6 bits;  conditional E-value: 5.2e-290
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               +kg++++++sl ++g +tvfGyPGG++lp+yd+lydsel+hilvrheq+aahaadGyarasG+vGv++a
  lcl|NCBI__GCF_000008645.1:WP_048061055.1   1 MKGGQAIIRSLLDQGADTVFGYPGGQLLPLYDMLYDSELKHILVRHEQCAAHAADGYARASGRVGVCIA 69 
                                               89******************************************************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatnlvtgiatay+ds+P+v+++Gqv+t+liG+dafqe+d++Git+p+tkhsf+ ++a+++p+i+
  lcl|NCBI__GCF_000008645.1:WP_048061055.1  70 TSGPGATNLVTGIATAYMDSAPIVAIAGQVPTHLIGNDAFQEVDMIGITMPITKHSFQPSDASEIPAIV 138
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               +++f+ia+tGrPGPv++dlPkd++e+ei+ ev+ ++elpgy+p+vkgh+lqik+a+eli++++kPv+l+
  lcl|NCBI__GCF_000008645.1:WP_048061055.1 139 RASFHIAKTGRPGPVVIDLPKDIQEQEIMEEVD-DLELPGYRPNVKGHPLQIKRAAELIRRSEKPVILA 206
                                               ****************************99998.9********************************** PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgGvii++as+e+kel++ +k+pvtttllG+G+fpedhp+a+gmlGmhG+k+anl+v+e+d+liavG+r
  lcl|NCBI__GCF_000008645.1:WP_048061055.1 207 GGGVIISGASREIKELSDLIKAPVTTTLLGKGSFPEDHPSAMGMLGMHGRKVANLTVDECDCLIAVGCR 275
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekiee 345
                                               f+dr+tgn+a+fap+a+iih+didPaeigknv vd+pivGda++vl+el++klk++ek++++Wle++++
  lcl|NCBI__GCF_000008645.1:WP_048061055.1 276 FSDRTTGNVAEFAPNARIIHVDIDPAEIGKNVGVDVPIVGDARNVLRELIAKLKKYEKRDSQWLESVQK 344
                                               ********************************************************************* PP

                                 TIGR00118 346 wkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGf 414
                                               ++++++++++++e ++kPq+vike+s++l+de++vttdvGq+qmw+a+fy++++prkfi+sgGlGtmGf
  lcl|NCBI__GCF_000008645.1:WP_048061055.1 345 FRADCMPRMSYDEVPLKPQQVIKEISQVLDDETVVTTDVGQNQMWMAHFYTSRAPRKFISSGGLGTMGF 413
                                               ********************************************************************* PP

                                 TIGR00118 415 GlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerys 483
                                               G+Paa+Gakva p+++vvav+Gdg+f m++q+l+ti+eydipv+i+i++n++lGmv+qWq+lfy+er+s
  lcl|NCBI__GCF_000008645.1:WP_048061055.1 414 GFPAAIGAKVALPDSDVVAVCGDGGFLMVCQDLATIREYDIPVVICIMDNRHLGMVAQWQRLFYDERMS 482
                                               ********************************************************************* PP

                                 TIGR00118 484 etklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGaglde 552
                                               +t+l+ e+pdfvklae++Gv+++rie+p e++e+l++a++s ep+lld+++d ++e+lPmv+pG+gl+e
  lcl|NCBI__GCF_000008645.1:WP_048061055.1 483 HTHLG-EVPDFVKLAESFGVEAERIEEPGETSEALSRAIRSGEPALLDIVID-PDEILPMVPPGCGLTE 549
                                               *****.7*********************************************.99************** PP

                                 TIGR00118 553 lvee 556
                                               +v+e
  lcl|NCBI__GCF_000008645.1:WP_048061055.1 550 IVGE 553
                                               *975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (574 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: 00:00:00.04
# Mc/sec: 7.89
//
[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