Alignments for a candidate for ilvI in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI 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::P9WG41
         (618 letters)



>FitnessBrowser__Miya:8501148
          Length = 615

 Score =  449 bits (1156), Expect = e-130
 Identities = 268/594 (45%), Positives = 341/594 (57%), Gaps = 24/594 (4%)

Query: 8   HSPTFKPEPHSAANEPKHPAARPKHVALQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPV 67
           H+P+ +  P +A+     P  R       Q  GA  VIR LE  G+DVI GIPGGA LP+
Sbjct: 4   HTPS-RTAPGTASGAAPTPRKR-------QPNGADLVIRLLERQGIDVIAGIPGGANLPL 55

Query: 68  YDPLFDSKKLRHVLVRHEQGAGHAASGYAHVTGRVGVCMATSGPGATNLVTPLADAQMDS 127
           YD L  +  +RHVL RHEQGAG  A G A VTGR  V  ATSGPGATN +T +ADA++DS
Sbjct: 56  YDALGRAGSIRHVLARHEQGAGFMAQGMARVTGRPAVFFATSGPGATNTLTAIADAKLDS 115

Query: 128 IPVVAITGQVGRGLIGTDAFQEADISGITMPITKHNFLVRSGDDIPRVLAEAFHIAASGR 187
           +PVV ITGQV  GL+G+DAFQE DI G+++P+TKHNFLVRS +++  V+  AF IAASGR
Sbjct: 116 VPVVCITGQVPLGLVGSDAFQEVDIYGMSIPVTKHNFLVRSVEELAEVIPAAFRIAASGR 175

Query: 188 PGAVLVDIPKDVLQG---QCTFSWPPRMELPGYKPNTKPHSRQVREAAKLIAAARKPVLY 244
           PG VLVDIPK+V      Q  F  PP+   P   P   P    +  AA L+ AA++P+LY
Sbjct: 176 PGPVLVDIPKNVQMAEVDQAVFDNPPQPGQPAAPP--APDPAGISRAAALLNAAQRPMLY 233

Query: 245 VGGGVIRGEATEQLRELAELTGIPVVTTLMARGAFPDSHRQNLGMPGMHGTVAAVAALQR 304
           +GGGV+   A++   +LAE  G+P V TLMA GA P  H  +LGM GMH        L  
Sbjct: 234 LGGGVVASGASDMAVQLAERAGLPTVMTLMALGAMPAGHPLSLGMLGMHAARHTNLLLAE 293

Query: 305 SDLLIALGTRFDDRVTGKLDSFAPEAKVIHADIDPAEIGKNRHADVPIVGDVKAVITELI 364
            D+L+  G RFDDR  GK + F P A +IH DID +E+ K       I GDV   + EL+
Sbjct: 294 CDVLLVAGARFDDRAVGKAERFCPGATIIHIDIDESELDKILPVHCGITGDVGLALAELL 353

Query: 365 AMLRHHHIPGTIEMADWWAYLNGVRKTYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFV 424
            +LR     G      W   +   R+ +P    P +D   +P  +I    +    DA+  
Sbjct: 354 PLLRTRAEAG---REAWLTRVEECRRRHPFVM-PGADDPRTPYGLIRCAADAVDHDAIVA 409

Query: 425 AGVGQHQMWAAQFIRYEKPRSWLNSGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQ 484
             VGQHQM  AQ      PR WL SGGLGTMGF +PAA+GA +A P   V    GDG  Q
Sbjct: 410 TDVGQHQMRTAQAYPLRGPRRWLTSGGLGTMGFGLPAAIGAALARPEATVLCFTGDGSLQ 469

Query: 485 MTNQELATCAVEGIPVKVALINNGNLGMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLA 544
           M  QELAT A EG+ VK+ L +N  LG+VRQ Q LFY  R     +A+   R  DF ++A
Sbjct: 470 MNIQELATAAEEGVNVKILLADNNALGLVRQQQELFYEGRL----VASTYRRKVDFARIA 525

Query: 545 EALGCVGLRCEREEDVV-DVINQARAINDCPVVIDFIVGADAQVWPMVAAGTSN 597
           E  G   +  +  E  + D+ +  RA   C  +I   V A A V+PMV  G  N
Sbjct: 526 EGFGVPAVDLDASEHPLRDLADALRAPGPC--LIRVTVPAGANVYPMVPPGADN 577


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: 1163
Number of extensions: 64
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: 618
Length of database: 615
Length adjustment: 37
Effective length of query: 581
Effective length of database: 578
Effective search space:   335818
Effective search space used:   335818
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.2059.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 10.62
//
[ok]

This GapMind analysis is from Apr 09 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