Alignments for a candidate for ilvI in Methanosarcina mazei Go1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Methanosarcina mazei Go1

Align acetohydroxy-acid synthase large subunit (EC 2.2.1.6) (characterized)
to candidate WP_011032621.1 MM_RS03495 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000007065.1:WP_011032621.1
          Length = 564

 Score =  597 bits (1539), Expect = e-175
 Identities = 308/579 (53%), Positives = 403/579 (69%), Gaps = 27/579 (4%)

Query: 1   MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60
           +NGA+A+IK LE E V+ LFGYPGG ++PFY+ L+ SDL H+L RHEQAAAHAADGYARA
Sbjct: 9   VNGAKALIKCLEKEGVDTLFGYPGGQIIPFYNELYDSDLRHILVRHEQAAAHAADGYARA 68

Query: 61  SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120
           +GK GVC+ TSGPGATNLVTG+ATA+ DS P+VALTGQVP  LIGNDAFQE D  G+ MP
Sbjct: 69  TGKTGVCVSTSGPGATNLVTGIATAYMDSVPIVALTGQVPRSLIGNDAFQEADITGITMP 128

Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180
           I KHN+ +Q   +IP I + AF IA TGRPGPV IDLPKDVQ +E+D+     P +V+L 
Sbjct: 129 ITKHNYLVQDPQEIPRIVKEAFHIASTGRPGPVLIDLPKDVQNIEIDLH---YPERVELR 185

Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240
           GY PT  G+ +QIK+A + IA++ RPII AGGGV+ S A+ EL++  E +  PV TTLMG
Sbjct: 186 GYKPTYKGNTQQIKRAAEEIANSCRPIIYAGGGVISSNASAELVEFAETIKAPVTTTLMG 245

Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHI 300
              I   HPL +GM+GMHG K ANY + ESD++I++G RF DR+TG ++SFA NA++IHI
Sbjct: 246 ISSIPTEHPLYVGMLGMHGCKYANYAIQESDLIIAVGARFDDRVTGKLESFAPNARVIHI 305

Query: 301 DIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNSLK 360
           D+DPAEI KNV V +PIVGDAK +LK +I+ +                 ++WIE VN  K
Sbjct: 306 DVDPAEISKNVKVHIPIVGDAKQVLKSLIRYVQCC------------RSAEWIEKVNLWK 353

Query: 361 KSSIPVMDYDDI--PIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTP 418
           K     ++Y +    I PQ +++++  V  D       II T+VGQ+QMW A +FK   P
Sbjct: 354 KEY--PLNYRECRDTIMPQFVIEQISEVCRD------AIIVTEVGQHQMWAAQFFKYSKP 405

Query: 419 RSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVIC 478
           R+FL+SGGLGTMG+GFP+A+GAKV +PD  VI I GDG F MN QEL T+ + +IPVV  
Sbjct: 406 RTFLTSGGLGTMGYGFPAAMGAKVGRPDKTVINIAGDGSFQMNSQELATVVQNDIPVVSV 465

Query: 479 IFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEA 538
           I +N  LGMV QWQ LFY +R       G+ DF+KLAE+YG    R E P+E+  A++EA
Sbjct: 466 ILNNGYLGMVRQWQELFYDRRYSYTFIKGSVDFVKLAEAYGALGLRAERPSEVRPAIEEA 525

Query: 539 INCDEPYLLDFAID-PSSALSMVPPGAKLTNIIDAVQEH 576
           +N   P +++  ++  ++   MVP GA +  IID ++EH
Sbjct: 526 VNSGRPTVVEVIVECEANVYPMVPAGAAINEIID-LEEH 563


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: 889
Number of extensions: 39
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: 599
Length of database: 564
Length adjustment: 36
Effective length of query: 563
Effective length of database: 528
Effective search space:   297264
Effective search space used:   297264
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_011032621.1 MM_RS03495 (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.29220.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-271  887.7   0.2   1.6e-271  887.5   0.2    1.0  1  lcl|NCBI__GCF_000007065.1:WP_011032621.1  MM_RS03495 acetolactate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000007065.1:WP_011032621.1  MM_RS03495 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  887.5   0.2  1.6e-271  1.6e-271       2     556 ..      10     560 ..       9     561 .. 0.99

  Alignments for each domain:
  == domain 1  score: 887.5 bits;  conditional E-value: 1.6e-271
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlat 70 
                                               +ga++l++ l+kegv+t+fGyPGG+++p+y++lyds+l+hilvrheqaaahaadGyara+Gk+Gv+++t
  lcl|NCBI__GCF_000007065.1:WP_011032621.1  10 NGAKALIKCLEKEGVDTLFGYPGGQIIPFYNELYDSDLRHILVRHEQAAAHAADGYARATGKTGVCVST 78 
                                               79******************************************************************* PP

                                 TIGR00118  71 sGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilk 139
                                               sGPGatnlvtgiatay+dsvP+v+ltGqv++sliG+dafqe+di+Git+p+tkh++lv++++++p+i+k
  lcl|NCBI__GCF_000007065.1:WP_011032621.1  79 SGPGATNLVTGIATAYMDSVPIVALTGQVPRSLIGNDAFQEADITGITMPITKHNYLVQDPQEIPRIVK 147
                                               ********************************************************************* PP

                                 TIGR00118 140 eafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvG 208
                                               eaf+iastGrPGPvl+dlPkdv++ ei+l+++e+vel+gykpt kg+++qik+a+e i+++ +P++++G
  lcl|NCBI__GCF_000007065.1:WP_011032621.1 148 EAFHIASTGRPGPVLIDLPKDVQNIEIDLHYPERVELRGYKPTYKGNTQQIKRAAEEIANSCRPIIYAG 216
                                               ********************************************************************* PP

                                 TIGR00118 209 gGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarf 277
                                               gGvi ++as+el+e+ae++k+pvtttl+G+ ++p +hpl +gmlGmhG+k+an+a++e+dl+iavGarf
  lcl|NCBI__GCF_000007065.1:WP_011032621.1 217 GGVISSNASAELVEFAETIKAPVTTTLMGISSIPTEHPLYVGMLGMHGCKYANYAIQESDLIIAVGARF 285
                                               ********************************************************************* PP

                                 TIGR00118 278 ddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieew 346
                                               ddrvtg+l++fap+a++ihid+dPaei+knvkv+ipivGdak+vl+ l++ ++  ++ e  W+ek++ w
  lcl|NCBI__GCF_000007065.1:WP_011032621.1 286 DDRVTGKLESFAPNARVIHIDVDPAEISKNVKVHIPIVGDAKQVLKSLIRYVQCCRSAE--WIEKVNLW 352
                                               **************************************************999988777..******** PP

                                 TIGR00118 347 kkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfG 415
                                               kkey+l++ e  ++i Pq vi+++s++ +d ai+ t+vGqhqmwaaqf+k++kpr+f+tsgGlGtmG+G
  lcl|NCBI__GCF_000007065.1:WP_011032621.1 353 KKEYPLNYRECRDTIMPQFVIEQISEVCRD-AIIVTEVGQHQMWAAQFFKYSKPRTFLTSGGLGTMGYG 420
                                               *****************************6.9999********************************** PP

                                 TIGR00118 416 lPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeeryse 484
                                               +Paa+Gakv+ p++tv++++Gdgsfqmn qel+t+v+ dipv+ vilnn +lGmv+qWqelfy++rys 
  lcl|NCBI__GCF_000007065.1:WP_011032621.1 421 FPAAMGAKVGRPDKTVINIAGDGSFQMNSQELATVVQNDIPVVSVILNNGYLGMVRQWQELFYDRRYSY 489
                                               ********************************************************************* PP

                                 TIGR00118 485 tklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldel 553
                                               t ++ ++ dfvklaeayG+ g+r e+p+e+  +++ea++s +p +++v v+ e++v+Pmv+ Ga+++e+
  lcl|NCBI__GCF_000007065.1:WP_011032621.1 490 TFIK-GSVDFVKLAEAYGALGLRAERPSEVRPAIEEAVNSGRPTVVEVIVECEANVYPMVPAGAAINEI 557
                                               ***9.69************************************************************** PP

                                 TIGR00118 554 vee 556
                                               ++ 
  lcl|NCBI__GCF_000007065.1:WP_011032621.1 558 IDL 560
                                               975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (564 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: 11.45
//
[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