GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvH in Echinicola vietnamensis KMM 6221, DSM 17526

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate Echvi_2056 Echvi_2056 acetolactate synthase, large subunit, biosynthetic type

Query= BRENDA::P9WG41
         (618 letters)



>lcl|FitnessBrowser__Cola:Echvi_2056 Echvi_2056 acetolactate
           synthase, large subunit, biosynthetic type
          Length = 564

 Score =  452 bits (1163), Expect = e-131
 Identities = 251/574 (43%), Positives = 349/574 (60%), Gaps = 25/574 (4%)

Query: 37  QLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFD-SKKLRHVLVRHEQGAGHAASGY 95
           ++ GA+ VI+SL     D IFG PGGA++PVYD L+D + +++HVL RHEQGA HAA GY
Sbjct: 5   RIRGAEIVIKSLVSENCDYIFGYPGGAIMPVYDALYDYADQIKHVLTRHEQGAIHAAQGY 64

Query: 96  AHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGI 155
           A V+G+VGVCMATSGPGATNL+T +ADA +DS P+V ITGQV   L+GTDAFQE D+ G 
Sbjct: 65  ARVSGKVGVCMATSGPGATNLITGIADALIDSTPLVCITGQVASALLGTDAFQETDVVGF 124

Query: 156 TMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRMELP 215
           +MP TK N  VR  +DI   +A+ FHIA SGRPG VL+DI KD       F++ P + + 
Sbjct: 125 SMPGTKWNIQVRKAEDIAPAIAKGFHIARSGRPGPVLIDITKDAQNELADFNYVPCLGIR 184

Query: 216 GYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLMA 275
            Y+P  K    ++  AA++I AA++P L  G GV+ G+A E+L+   + TGIP   TL+ 
Sbjct: 185 SYRPYPKVKDSEIAAAAEVINAAKRPYLLFGQGVVIGKAEEELKAFLDKTGIPAACTLLG 244

Query: 276 RGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKVIHA 335
            GA  + H Q +G  GMHG  A      + D+LIA+G RFDDRVTG L  +A +AKV+H 
Sbjct: 245 SGALSEEHPQFVGKLGMHGNYAPNILTNKCDVLIAVGMRFDDRVTGDLKRYAKQAKVVHL 304

Query: 336 DIDPAEIGKNRHADVPIVGDVK---AVITELIAMLRHHHIPGTIEMADWWAYLNGVRK-- 390
           ++D AEI KN   +V ++G+ K    ++TE +    H          +W A    + +  
Sbjct: 305 ELDNAEINKNVKCEVSVLGNCKESLPMLTEKVNKASHD---------EWLAEFRTLEEKE 355

Query: 391 ---TYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWL 447
                 L   P   G L+   VI  + +    DAV V  VGQHQM A ++ +++  R+ +
Sbjct: 356 KSAVVSLDLLPTKTG-LTMGEVIRYINDYKKDDAVLVTDVGQHQMIAWRYFKFKTTRTQV 414

Query: 448 NSGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINN 507
            SGGLGTMGF++PAA+GA++A    +V  + GDG  QMT QEL T      PVKV L+NN
Sbjct: 415 TSGGLGTMGFSLPAALGAQLADLNRQVVCVVGDGGIQMTVQELGTIMQTRSPVKVVLLNN 474

Query: 508 GNLGMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQA 567
             LGMVRQWQ LF+ +RYS T+L       PDF+K+AEA      +     D+ D +   
Sbjct: 475 NFLGMVRQWQQLFFDKRYSFTELDN-----PDFIKIAEAYNMKATKVTERGDLSDAVAD- 528

Query: 568 RAINDCPVVIDFIVGADAQVWPMVAAGTSNDEIQ 601
              ++ P  ++ +V  +  V+PM+  G S +E++
Sbjct: 529 MLTHEGPYFLEVVVEKEDNVFPMIPTGCSVEEVR 562


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: 880
Number of extensions: 35
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: 618
Length of database: 564
Length adjustment: 37
Effective length of query: 581
Effective length of database: 527
Effective search space:   306187
Effective search space used:   306187
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 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.29650.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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.18
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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:

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:

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:

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 preprint on GapMind for carbon sources, or view the source code, or see 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