GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvH in Desulfovibrio vulgaris Miyazaki F

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate 8501148 DvMF_1883 acetolactate synthase catalytic subunit (RefSeq)

Query= BRENDA::P08142
         (562 letters)



>lcl|FitnessBrowser__Miya:8501148 DvMF_1883 acetolactate synthase
           catalytic subunit (RefSeq)
          Length = 615

 Score =  645 bits (1665), Expect = 0.0
 Identities = 331/569 (58%), Positives = 411/569 (72%), Gaps = 9/569 (1%)

Query: 2   ASSGTTSTRKRF-TGAEFIVHFLEQQGIKIVTGIPGGSILPVYDALSQSTQIRHILARHE 60
           AS    + RKR   GA+ ++  LE+QGI ++ GIPGG+ LP+YDAL ++  IRH+LARHE
Sbjct: 14  ASGAAPTPRKRQPNGADLVIRLLERQGIDVIAGIPGGANLPLYDALGRAGSIRHVLARHE 73

Query: 61  QGAGFIAQGMARTDGKPAVCMACSGPGATNLVTAIADARLDSIPLICITGQVPASMIGTD 120
           QGAGF+AQGMAR  G+PAV  A SGPGATN +TAIADA+LDS+P++CITGQVP  ++G+D
Sbjct: 74  QGAGFMAQGMARVTGRPAVFFATSGPGATNTLTAIADAKLDSVPVVCITGQVPLGLVGSD 133

Query: 121 AFQEVDTYGISIPITKHNYLVRHIEELPQVMSDAFRIAQSGRPGPVWIDIPKDVQTAVFE 180
           AFQEVD YG+SIP+TKHN+LVR +EEL +V+  AFRIA SGRPGPV +DIPK+VQ A  +
Sbjct: 134 AFQEVDIYGMSIPVTKHNFLVRSVEELAEVIPAAFRIAASGRPGPVLVDIPKNVQMAEVD 193

Query: 181 ---IETQPAMAEKAAAPAFSEESIRDAAAMINAAKRPVLYLGGGVINAPAR--VRELAEK 235
               +  P   + AA PA     I  AAA++NAA+RP+LYLGGGV+ + A     +LAE+
Sbjct: 194 QAVFDNPPQPGQPAAPPAPDPAGISRAAALLNAAQRPMLYLGGGVVASGASDMAVQLAER 253

Query: 236 AQLPTTMTLMALGMLPKAHPLSLGMLGMHGVRSTNYILQEADLLIVLGARFDDRAIGKTE 295
           A LPT MTLMALG +P  HPLSLGMLGMH  R TN +L E D+L+V GARFDDRA+GK E
Sbjct: 254 AGLPTVMTLMALGAMPAGHPLSLGMLGMHAARHTNLLLAECDVLLVAGARFDDRAVGKAE 313

Query: 296 QFCPNAKIIHVDIDRAELGKIKQPHVAIQADVDDVLAQLIPLVEAQPRA---EWHQLVAD 352
           +FCP A IIH+DID +EL KI   H  I  DV   LA+L+PL+  +  A    W   V +
Sbjct: 314 RFCPGATIIHIDIDESELDKILPVHCGITGDVGLALAELLPLLRTRAEAGREAWLTRVEE 373

Query: 353 LQREFPCPIPKACDPLSHYGLINAVAACVDDNAIITTDVGQHQMWTAQAYPLNRPRQWLT 412
            +R  P  +P A DP + YGLI   A  VD +AI+ TDVGQHQM TAQAYPL  PR+WLT
Sbjct: 374 CRRRHPFVMPGADDPRTPYGLIRCAADAVDHDAIVATDVGQHQMRTAQAYPLRGPRRWLT 433

Query: 413 SGGLGTMGFGLPAAIGAALANPDRKVLCFSGDGSLMMNIQEMATASENQLDVKIILMNNE 472
           SGGLGTMGFGLPAAIGAALA P+  VLCF+GDGSL MNIQE+ATA+E  ++VKI+L +N 
Sbjct: 434 SGGLGTMGFGLPAAIGAALARPEATVLCFTGDGSLQMNIQELATAAEEGVNVKILLADNN 493

Query: 473 ALGLVHQQQSLFYEQGVFAATYPGKINFMQIAAGFGLETCDLNNEADPQASLQEIINRPG 532
           ALGLV QQQ LFYE  + A+TY  K++F +IA GFG+   DL+    P   L + +  PG
Sbjct: 494 ALGLVRQQQELFYEGRLVASTYRRKVDFARIAEGFGVPAVDLDASEHPLRDLADALRAPG 553

Query: 533 PALIHVRIDAEEKVYPMVPPGAANTEMVG 561
           P LI V + A   VYPMVPPGA N +M+G
Sbjct: 554 PCLIRVTVPAGANVYPMVPPGADNLQMIG 582


Lambda     K      H
   0.320    0.135    0.400 

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: 1115
Number of extensions: 52
Number of successful extensions: 5
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: 562
Length of database: 615
Length adjustment: 37
Effective length of query: 525
Effective length of database: 578
Effective search space:   303450
Effective search space used:   303450
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 8501148 DvMF_1883 (acetolactate synthase catalytic subunit (RefSeq))
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.29715.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.9e-195  634.6   0.0     8e-195  634.4   0.0    1.0  1  lcl|FitnessBrowser__Miya:8501148  DvMF_1883 acetolactate synthase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501148  DvMF_1883 acetolactate synthase catalytic subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  634.4   0.0    8e-195    8e-195       2     555 ..      27     582 ..      26     584 .. 0.98

  Alignments for each domain:
  == domain 1  score: 634.4 bits;  conditional E-value: 8e-195
                         TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGatn 77 
                                       +ga+++++ l+++g++++ G+PGGa lp+ydal  ++ ++h+l+rheq+a  +a+G+ar++G++ v +atsGPGatn
  lcl|FitnessBrowser__Miya:8501148  27 NGADLVIRLLERQGIDVIAGIPGGANLPLYDALGrAGSIRHVLARHEQGAGFMAQGMARVTGRPAVFFATSGPGATN 103
                                       599******************************9899**************************************** PP

                         TIGR00118  78 lvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPvl 154
                                       ++t+ia+a ldsvP+v +tGqv+  l+Gsdafqe+di G+++pvtkh+flv+++e+l+e++ +af ia++GrPGPvl
  lcl|FitnessBrowser__Miya:8501148 104 TLTAIADAKLDSVPVVCITGQVPLGLVGSDAFQEVDIYGMSIPVTKHNFLVRSVEELAEVIPAAFRIAASGRPGPVL 180
                                       ***************************************************************************** PP

                         TIGR00118 155 vdlPkdvteaeieleveekvelpgykpt.vkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlkip 230
                                       vd+Pk+v+ ae+++ v ++   pg       ++++ i +a+ l+++a++P+l+ GgGv++++as+  ++laer+ +p
  lcl|FitnessBrowser__Miya:8501148 181 VDIPKNVQMAEVDQAVFDNPPQPGQPAApPAPDPAGISRAAALLNAAQRPMLYLGGGVVASGASDMAVQLAERAGLP 257
                                       ****************99999999754415789999***************************************** PP

                         TIGR00118 231 vtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigkn 307
                                        ++tl+ lGa+p+ hpl+lgmlGmh ++++nl + e+d+l+  Garfddr  g+ ++f+p a+iihidid +e++k+
  lcl|FitnessBrowser__Miya:8501148 258 TVMTLMALGAMPAGHPLSLGMLGMHAARHTNLLLAECDVLLVAGARFDDRAVGKAERFCPGATIIHIDIDESELDKI 334
                                       ***************************************************************************** PP

                         TIGR00118 308 vkvdipivGdakkvleellkklkeeekkeke.WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttd 383
                                       + v+  i Gd+   l+ell  l+++ +  +e Wl ++ee ++++++ +   +++  P  +i+     ++++aiv+td
  lcl|FitnessBrowser__Miya:8501148 335 LPVHCGITGDVGLALAELLPLLRTRAEAGREaWLTRVEECRRRHPFVMPGADDPRTPYGLIRCAADAVDHDAIVATD 411
                                       **********************9997766666********************************************* PP

                         TIGR00118 384 vGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkiv 460
                                       vGqhqm +aq y+ + pr+++tsgGlGtmGfGlPaa+Ga +a pe+tv++ tGdgs+qmn+qel+t++e +++vki+
  lcl|FitnessBrowser__Miya:8501148 412 VGQHQMRTAQAYPLRGPRRWLTSGGLGTMGFGLPAAIGAALARPEATVLCFTGDGSLQMNIQELATAAEEGVNVKIL 488
                                       ***************************************************************************** PP

                         TIGR00118 461 ilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdke 537
                                       + +n+ lG+v+q qelfye+r  +++    + df+++ae++Gv ++ +   e     l++al+  +p l+ v+v   
  lcl|FitnessBrowser__Miya:8501148 489 LADNNALGLVRQQQELFYEGRLVASTYRR-KVDFARIAEGFGVPAVDLDASEHPLRDLADALRAPGPCLIRVTVPAG 564
                                       *************************9995.9********************************************** PP

                         TIGR00118 538 eevlPmvapGagldelve 555
                                       ++v+Pmv+pGa + ++++
  lcl|FitnessBrowser__Miya:8501148 565 ANVYPMVPPGADNLQMIG 582
                                       ***********9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (615 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: 8.29
//
[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 paper from 2022 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