Alignments for a candidate for ilvI in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Echinicola vietnamensis KMM 6221, DSM 17526

Align acetohydroxy-acid synthase large subunit (EC 2.2.1.6) (characterized)
to candidate Echvi_2056 Echvi_2056 acetolactate synthase, large subunit, biosynthetic type

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



>FitnessBrowser__Cola:Echvi_2056
          Length = 564

 Score =  452 bits (1164), Expect = e-131
 Identities = 241/573 (42%), Positives = 353/573 (61%), Gaps = 21/573 (3%)

Query: 1   MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALH-HSDLI-HLLTRHEQAAAHAADGYA 58
           + GAE +IK+L +E  + +FGYPGGA++P YDAL+ ++D I H+LTRHEQ A HAA GYA
Sbjct: 6   IRGAEIVIKSLVSENCDYIFGYPGGAIMPVYDALYDYADQIKHVLTRHEQGAIHAAQGYA 65

Query: 59  RASGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLF 118
           R SGKVGVC+ TSGPGATNL+TG+A A  DS+P+V +TGQV + L+G DAFQE D +G  
Sbjct: 66  RVSGKVGVCMATSGPGATNLITGIADALIDSTPLVCITGQVASALLGTDAFQETDVVGFS 125

Query: 119 MPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVK 178
           MP  K N Q++K   I       F IA++GRPGPV ID+ KD Q    D +  P    + 
Sbjct: 126 MPGTKWNIQVRKAEDIAPAIAKGFHIARSGRPGPVLIDITKDAQNELADFNYVPC---LG 182

Query: 179 LIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTL 238
           +  Y P       +I  A ++I +AKRP +L G GV++  A EEL   ++   IP   TL
Sbjct: 183 IRSYRPYPKVKDSEIAAAAEVINAAKRPYLLFGQGVVIGKAEEELKAFLDKTGIPAACTL 242

Query: 239 MGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKII 298
           +G G +SE HP  +G +GMHG    N   ++ DVLI++G RF DR+TGD+K +A  AK++
Sbjct: 243 LGSGALSEEHPQFVGKLGMHGNYAPNILTNKCDVLIAVGMRFDDRVTGDLKRYAKQAKVV 302

Query: 299 HIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNS 358
           H+++D AEI KNV  +V ++G+     KE +  L   +NK S +        +W+    +
Sbjct: 303 HLELDNAEINKNVKCEVSVLGNC----KESLPMLTEKVNKASHD--------EWLAEFRT 350

Query: 359 L-KKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQT 417
           L +K    V+  D +P K    + E++  I+D     + ++ TDVGQ+QM    YFK +T
Sbjct: 351 LEEKEKSAVVSLDLLPTKTGLTMGEVIRYINDYK-KDDAVLVTDVGQHQMIAWRYFKFKT 409

Query: 418 PRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVI 477
            R+ ++SGGLGTMGF  P+A+GA++A  + +V+C+ GDGG  M  QELGTI +   PV +
Sbjct: 410 TRTQVTSGGLGTMGFSLPAALGAQLADLNRQVVCVVGDGGIQMTVQELGTIMQTRSPVKV 469

Query: 478 CIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKE 537
            + +N  LGMV QWQ LF+ KR         PDFIK+AE+Y +KA ++    ++++A+ +
Sbjct: 470 VLLNNNFLGMVRQWQQLFFDKRYSFTELDN-PDFIKIAEAYNMKATKVTERGDLSDAVAD 528

Query: 538 AINCDEPYLLDFAID-PSSALSMVPPGAKLTNI 569
            +  + PY L+  ++   +   M+P G  +  +
Sbjct: 529 MLTHEGPYFLEVVVEKEDNVFPMIPTGCSVEEV 561


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: 801
Number of extensions: 43
Number of successful extensions: 6
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 Echvi_2056 Echvi_2056 (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.17883.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   2.9e-218  711.7   0.2   3.3e-218  711.6   0.2    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2056  Echvi_2056 acetolactate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2056  Echvi_2056 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  711.6   0.2  3.3e-218  3.3e-218       2     553 ..       7     561 ..       6     564 .] 0.97

  Alignments for each domain:
  == domain 1  score: 711.6 bits;  conditional E-value: 3.3e-218
                            TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly..dselehilvrheqaaahaadGyarasGkvGvvlatsGP 73 
                                          +gaei+++sl +e+ +++fGyPGGa++p+ydaly  +++++h+l+rheq+a+haa+Gyar+sGkvGv++atsGP
  lcl|FitnessBrowser__Cola:Echvi_2056   7 RGAEIVIKSLVSENCDYIFGYPGGAIMPVYDALYdyADQIKHVLTRHEQGAIHAAQGYARVSGKVGVCMATSGP 80 
                                          79********************************989************************************* PP

                            TIGR00118  74 GatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiast 147
                                          Gatnl+tgia+a +ds+Plv +tGqva++l+G+dafqe d++G ++p tk++++v+kaed++  + + f+ia +
  lcl|FitnessBrowser__Cola:Echvi_2056  81 GATNLITGIADALIDSTPLVCITGQVASALLGTDAFQETDVVGFSMPGTKWNIQVRKAEDIAPAIAKGFHIARS 154
                                          ************************************************************************** PP

                            TIGR00118 148 GrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelk 221
                                          GrPGPvl+d+ kd +++  ++++   + +++y+p  k +   i++a+e+i++ak+P ll G Gv+i++a+eelk
  lcl|FitnessBrowser__Cola:Echvi_2056 155 GRPGPVLIDITKDAQNELADFNYVPCLGIRSYRPYPKVKDSEIAAAAEVINAAKRPYLLFGQGVVIGKAEEELK 228
                                          ************************************************************************** PP

                            TIGR00118 222 elaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakii 295
                                           + +++ ip ++tllG Ga+ e+hp+++g lGmhG ++ n+  +++d+liavG+rfddrvtg+l+++a++ak++
  lcl|FitnessBrowser__Cola:Echvi_2056 229 AFLDKTGIPAACTLLGSGALSEEHPQFVGKLGMHGNYAPNILTNKCDVLIAVGMRFDDRVTGDLKRYAKQAKVV 302
                                          ************************************************************************** PP

                            TIGR00118 296 hididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkey...ilklde..eeesikPq 364
                                          h+++d aei+knvk ++++ G++k+ l  l +k+++ +++e  Wl++ + + ++    +++ld   +++ +   
  lcl|FitnessBrowser__Cola:Echvi_2056 303 HLELDNAEINKNVKCEVSVLGNCKESLPMLTEKVNKASHDE--WLAEFRTLEEKEksaVVSLDLlpTKTGLTMG 374
                                          ***********************************999888..99887776554411144455422677799** PP

                            TIGR00118 365 kvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdg 438
                                          +vi+ +    kd+a++ tdvGqhqm a +++k+k++r+ +tsgGlGtmGf lPaalGa++a  + +vv+v+Gdg
  lcl|FitnessBrowser__Cola:Echvi_2056 375 EVIRYINDYKKDDAVLVTDVGQHQMIAWRYFKFKTTRTQVTSGGLGTMGFSLPAALGAQLADLNRQVVCVVGDG 448
                                          ************************************************************************** PP

                            TIGR00118 439 sfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpe 512
                                          ++qm++qel ti++   pvk+v+lnn++lGmv+qWq+lf+++rys t+l +  pdf+k+aeay +k+++++++ 
  lcl|FitnessBrowser__Cola:Echvi_2056 449 GIQMTVQELGTIMQTRSPVKVVLLNNNFLGMVRQWQQLFFDKRYSFTELDN--PDFIKIAEAYNMKATKVTERG 520
                                          *************************************************97..********************* PP

                            TIGR00118 513 eleeklkealeskepvlldvevdkeeevlPmvapGagldel 553
                                          +l+++++++l++++p++l+v+v+ke++v+Pm+++G++++e+
  lcl|FitnessBrowser__Cola:Echvi_2056 521 DLSDAVADMLTHEGPYFLEVVVEKEDNVFPMIPTGCSVEEV 561
                                          *************************************9986 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: 00:00:00.03
# Mc/sec: 9.31
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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