Alignments for a candidate for ilvI in Methanosarcina acetivorans C2A

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Methanosarcina acetivorans C2A

Align acetohydroxy-acid synthase large subunit (EC 2.2.1.6) (characterized)
to candidate WP_011023692.1 MA_RS19755 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000007345.1:WP_011023692.1
          Length = 564

 Score =  605 bits (1559), Expect = e-177
 Identities = 314/578 (54%), Positives = 403/578 (69%), Gaps = 24/578 (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+ +P
Sbjct: 69  TGKTGVCVSTSGPGATNLVTGIATAYMDSVPIVALTGQVPRPLIGNDAFQEADITGITLP 128

Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180
           I KHN+ +Q   +IP I + AF IA TGRPGPV IDLPKDVQ +E+D+     P KV+L 
Sbjct: 129 ITKHNYLVQDAEEIPRIVKEAFHIASTGRPGPVLIDLPKDVQNIEIDLQ---YPDKVELR 185

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

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

Query: 301 DIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNSLK 360
           D+DPAEI KNV V VPIVGDAK ILK +IK +             + N ++WIE +N  K
Sbjct: 306 DVDPAEISKNVKVHVPIVGDAKQILKSLIKYI------------QRCNSAEWIEKINQWK 353

Query: 361 KSSIPVMDY-DDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPR 419
           K       Y     I PQ +V+++  V       K+ II T+VGQ+QMW A YFK + PR
Sbjct: 354 KEYPLAYRYVSSDTIMPQFVVEQISEVC------KDAIIVTEVGQHQMWAAQYFKYRKPR 407

Query: 420 SFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVICI 479
           +FL+SGGLGTMG+G P+A+GAKV KPD  VI I GDG F MN QEL T+ + +IPVV  I
Sbjct: 408 TFLTSGGLGTMGYGLPAAMGAKVGKPDKTVINIAGDGSFQMNSQELATLVQNDIPVVSVI 467

Query: 480 FDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEAI 539
            +N  LGMV QWQ LFY +R       G+ DF+KLAE+YG    R E P+E+  A++EA+
Sbjct: 468 LNNGYLGMVRQWQELFYDRRYSHTFIKGSVDFVKLAEAYGALGLRAEKPSEVRPAIEEAV 527

Query: 540 NCDEPYLLDFAID-PSSALSMVPPGAKLTNIIDAVQEH 576
               P +++  ++  ++   MVP GA +  IID ++EH
Sbjct: 528 GSGRPAVVEVIVECEANVYPMVPAGAAINEIID-LEEH 564


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: 890
Number of extensions: 37
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_011023692.1 MA_RS19755 (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.4010.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.9e-272  889.0   0.8   6.9e-272  888.8   0.8    1.0  1  lcl|NCBI__GCF_000007345.1:WP_011023692.1  MA_RS19755 acetolactate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000007345.1:WP_011023692.1  MA_RS19755 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  888.8   0.8  6.9e-272  6.9e-272       2     556 ..      10     561 ..       9     562 .. 0.99

  Alignments for each domain:
  == domain 1  score: 888.8 bits;  conditional E-value: 6.9e-272
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlat 70 
                                               +ga++l++ l+kegv+t+fGyPGG+++p+y++lyds+l+hilvrheqaaahaadGyara+Gk+Gv+++t
  lcl|NCBI__GCF_000007345.1:WP_011023692.1  10 NGAKALIKCLEKEGVDTLFGYPGGQIIPFYNELYDSDLRHILVRHEQAAAHAADGYARATGKTGVCVST 78 
                                               79******************************************************************* PP

                                 TIGR00118  71 sGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilk 139
                                               sGPGatnlvtgiatay+dsvP+v+ltGqv++ liG+dafqe+di+Gitlp+tkh++lv++ae++p+i+k
  lcl|NCBI__GCF_000007345.1:WP_011023692.1  79 SGPGATNLVTGIATAYMDSVPIVALTGQVPRPLIGNDAFQEADITGITLPITKHNYLVQDAEEIPRIVK 147
                                               ********************************************************************* PP

                                 TIGR00118 140 eafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvG 208
                                               eaf+iastGrPGPvl+dlPkdv++ ei+l++++kvel+gykpt kg+++qik+a+e i+++ +P++++G
  lcl|NCBI__GCF_000007345.1:WP_011023692.1 148 EAFHIASTGRPGPVLIDLPKDVQNIEIDLQYPDKVELRGYKPTYKGNTQQIKRAAEEIANSCRPIIYAG 216
                                               ********************************************************************* PP

                                 TIGR00118 209 gGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarf 277
                                               gGvi ++as+el+elae+l +pvtttl+G+ a+p +hpl +gmlGmhG+k+an+av+e+dl+iavGarf
  lcl|NCBI__GCF_000007345.1:WP_011023692.1 217 GGVISSNASAELVELAETLMAPVTTTLMGISAIPTEHPLYVGMLGMHGCKYANYAVQESDLIIAVGARF 285
                                               ********************************************************************* PP

                                 TIGR00118 278 ddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieew 346
                                               ddrvtg+l++fap+a++ihid+dPaei+knvkv++pivGdak++l+ l+k +++ ++ e  W+eki++w
  lcl|NCBI__GCF_000007345.1:WP_011023692.1 286 DDRVTGKLESFAPNARVIHIDVDPAEISKNVKVHVPIVGDAKQILKSLIKYIQRCNSAE--WIEKINQW 352
                                               ****************************************************9998888..******** PP

                                 TIGR00118 347 kkeyilklde.eeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGf 414
                                               kkey+l++ + ++++i Pq v++++s++ kd ai+ t+vGqhqmwaaq++k++kpr+f+tsgGlGtmG+
  lcl|NCBI__GCF_000007345.1:WP_011023692.1 353 KKEYPLAYRYvSSDTIMPQFVVEQISEVCKD-AIIVTEVGQHQMWAAQYFKYRKPRTFLTSGGLGTMGY 420
                                               *******87725677***************6.9999********************************* PP

                                 TIGR00118 415 GlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerys 483
                                               GlPaa+Gakv+kp++tv++++Gdgsfqmn qel+t+v+ dipv+ vilnn +lGmv+qWqelfy++rys
  lcl|NCBI__GCF_000007345.1:WP_011023692.1 421 GLPAAMGAKVGKPDKTVINIAGDGSFQMNSQELATLVQNDIPVVSVILNNGYLGMVRQWQELFYDRRYS 489
                                               ********************************************************************* PP

                                 TIGR00118 484 etklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGaglde 552
                                               +t ++ ++ dfvklaeayG+ g+r ekp+e+  +++ea+ s +p++++v v+ e++v+Pmv+ Ga+++e
  lcl|NCBI__GCF_000007345.1:WP_011023692.1 490 HTFIK-GSVDFVKLAEAYGALGLRAEKPSEVRPAIEEAVGSGRPAVVEVIVECEANVYPMVPAGAAINE 557
                                               ****9.69************************************************************* PP

                                 TIGR00118 553 lvee 556
                                               +++ 
  lcl|NCBI__GCF_000007345.1:WP_011023692.1 558 IIDL 561
                                               *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: 11.85
//
[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