Aligments for a candidate for ilvH in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Aligments for a candidate for ilvH in Desulfovibrio vulgaris Hildenborough

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate 209294 DVU0360 acetolactate synthase, large subunit, biosynthetic type

Query= BRENDA::P08142
         (562 letters)



>MicrobesOnline__882:209294
          Length = 563

 Score =  679 bits (1752), Expect = 0.0
 Identities = 339/552 (61%), Positives = 415/552 (75%), Gaps = 2/552 (0%)

Query: 12  RFTGAEFIVHFLEQQGIKIVTGIPGGSILPVYDALSQSTQIRHILARHEQGAGFIAQGMA 71
           R +GAE ++  LE+QGI  ++GIPGG+ LP+YDALS S +IRH+LARHEQGAGFIAQGMA
Sbjct: 3   RMSGAELVIRLLERQGIDCISGIPGGANLPLYDALSHSKRIRHVLARHEQGAGFIAQGMA 62

Query: 72  RTDGKPAVCMACSGPGATNLVTAIADARLDSIPLICITGQVPASMIGTDAFQEVDTYGIS 131
           R+ G+PAV  A SGPGATN +TAIADA+LDS+P+ICITGQVP SMIG+DAFQEVD YG+S
Sbjct: 63  RSTGRPAVFFATSGPGATNTLTAIADAKLDSVPVICITGQVPRSMIGSDAFQEVDIYGMS 122

Query: 132 IPITKHNYLVRHIEELPQVMSDAFRIAQSGRPGPVWIDIPKDVQTAVFEIETQPAMAEKA 191
           IP+TKHN+LVR +E+L  V+ +AFRIA SGRPGPV +DIPKDVQTA    E  P      
Sbjct: 123 IPVTKHNFLVRSVEDLLTVIPEAFRIATSGRPGPVLVDIPKDVQTAEVAFEAWPETGGPD 182

Query: 192 AAPAFSEESIRDAAAMINAAKRPVLYLGGGVINAPAR--VRELAEKAQLPTTMTLMALGM 249
            A A   E +  AA M+  A+RP+L++GGGV+ + A    R  AE+  LPT M+L+ LG 
Sbjct: 183 PAEAPDMEGLARAARMLAEAERPILFIGGGVVASGAGEVARVFAERTGLPTAMSLLGLGT 242

Query: 250 LPKAHPLSLGMLGMHGVRSTNYILQEADLLIVLGARFDDRAIGKTEQFCPNAKIIHVDID 309
           LP  HPL+LGMLGMHG R TN +L+E DLL+V+GARFDDRA G+ EQFCP+A IIHVDID
Sbjct: 243 LPPEHPLTLGMLGMHGARCTNMLLEECDLLMVVGARFDDRATGRIEQFCPHASIIHVDID 302

Query: 310 RAELGKIKQPHVAIQADVDDVLAQLIPLVEAQPRAEWHQLVADLQREFPCPIPKACDPLS 369
            +E+ K++  HVAI  D   VL  L+P++E   R  WH  VA ++   P   P A DP +
Sbjct: 303 PSEIDKLRTAHVAITGDAGRVLEALLPMLEPVDRKAWHGHVARMKAAHPLLTPGADDPRT 362

Query: 370 HYGLINAVAACVDDNAIITTDVGQHQMWTAQAYPLNRPRQWLTSGGLGTMGFGLPAAIGA 429
            YGL+   AAC+DD+AII TDVGQHQM TAQAYPL R RQWLTSGGLGTMGFGLPAAIGA
Sbjct: 363 PYGLVTCTAACLDDSAIIATDVGQHQMRTAQAYPLRRTRQWLTSGGLGTMGFGLPAAIGA 422

Query: 430 ALANPDRKVLCFSGDGSLMMNIQEMATASENQLDVKIILMNNEALGLVHQQQSLFYEQGV 489
           ALANP+R V+CF+GDGSL MNIQE+ATA+E   +VKI+L NN ALGLV QQQ LFY + +
Sbjct: 423 ALANPERTVVCFTGDGSLQMNIQELATAAETGANVKIVLANNNALGLVQQQQDLFYGRRI 482

Query: 490 FAATYPGKINFMQIAAGFGLETCDLNNEADPQASLQEIINRPGPALIHVRIDAEEKVYPM 549
           FA+ +  +I+F++IA GFG+   DL   ADP+  L   +   GP LIHV +  EE VYPM
Sbjct: 483 FASDFTHRIDFVRIAEGFGVPAVDLGRSADPKRDLARALRAKGPCLIHVPVAVEENVYPM 542

Query: 550 VPPGAANTEMVG 561
           VPPGAANTEM+G
Sbjct: 543 VPPGAANTEMIG 554


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: 954
Number of extensions: 35
Number of successful extensions: 2
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: 563
Length adjustment: 36
Effective length of query: 526
Effective length of database: 527
Effective search space:   277202
Effective search space used:   277202
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 209294 DVU0360 (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.29978.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.3e-205  670.0   0.0   1.5e-205  669.8   0.0    1.0  1  lcl|MicrobesOnline__882:209294  DVU0360 acetolactate synthase, l


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:209294  DVU0360 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  669.8   0.0  1.5e-205  1.5e-205       1     555 [.       4     554 ..       4     556 .. 0.98

  Alignments for each domain:
  == domain 1  score: 669.8 bits;  conditional E-value: 1.5e-205
                       TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGatnl 78 
                                     ++gae++++ l+++g++ + G+PGGa lp+ydal  ++ ++h+l+rheq+a  +a+G+ar++G++ v +atsGPGatn+
  lcl|MicrobesOnline__882:209294   4 MSGAELVIRLLERQGIDCISGIPGGANLPLYDALShSKRIRHVLARHEQGAGFIAQGMARSTGRPAVFFATSGPGATNT 82 
                                     79********************************75889**************************************** PP

                       TIGR00118  79 vtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPvlvdl 157
                                     +t+ia+a ldsvP++ +tGqv++s+iGsdafqe+di G+++pvtkh+flv+++edl +++ eaf ia++GrPGPvlvd+
  lcl|MicrobesOnline__882:209294  83 LTAIADAKLDSVPVICITGQVPRSMIGSDAFQEVDIYGMSIPVTKHNFLVRSVEDLLTVIPEAFRIATSGRPGPVLVDI 161
                                     ******************************************************************************* PP

                       TIGR00118 158 PkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlkipvtttll 236
                                     Pkdv++ae+ +e     e  g  p   ++   +++a+ ++++a++P+l++GgGv++++a e  + +aer+ +p +++ll
  lcl|MicrobesOnline__882:209294 162 PKDVQTAEVAFEAWP--ETGGPDPAEAPDMEGLARAARMLAEAERPILFIGGGVVASGAGEVARVFAERTGLPTAMSLL 238
                                     **********99885..556889999999************************************************** PP

                       TIGR00118 237 GlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigknvkvdipiv 315
                                     GlG++p +hpl+lgmlGmhG++ +n+ ++e+dll+ vGarfddr tg +++f+p+a iih+didP+ei+k ++++++i 
  lcl|MicrobesOnline__882:209294 239 GLGTLPPEHPLTLGMLGMHGARCTNMLLEECDLLMVVGARFDDRATGRIEQFCPHASIIHVDIDPSEIDKLRTAHVAIT 317
                                     ******************************************************************************* PP

                       TIGR00118 316 GdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqf 394
                                     Gda +vle ll  l+ +++k   W  +++++k+ ++l     +++  P  ++      l+d+ai++tdvGqhqm +aq 
  lcl|MicrobesOnline__882:209294 318 GDAGRVLEALLPMLEPVDRKA--WHGHVARMKAAHPLLTPGADDPRTPYGLVTCTAACLDDSAIIATDVGQHQMRTAQA 394
                                     ****************99998..******************************************************** PP

                       TIGR00118 395 yktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473
                                     y+ +++r+++tsgGlGtmGfGlPaa+Ga +a+pe tvv+ tGdgs+qmn+qel+t++e + +vkiv+ nn+ lG+v+q 
  lcl|MicrobesOnline__882:209294 395 YPLRRTRQWLTSGGLGTMGFGLPAAIGAALANPERTVVCFTGDGSLQMNIQELATAAETGANVKIVLANNNALGLVQQQ 473
                                     ******************************************************************************* PP

                       TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGaglde 552
                                     q+lfy +r  ++ +++   dfv++ae++Gv ++ + + ++ +  l++al+ k+p l+ v v+ ee+v+Pmv+pGa+++e
  lcl|MicrobesOnline__882:209294 474 QDLFYGRRIFASDFTH-RIDFVRIAEGFGVPAVDLGRSADPKRDLARALRAKGPCLIHVPVAVEENVYPMVPPGAANTE 551
                                     ***************5.9************************************************************* PP

                       TIGR00118 553 lve 555
                                     +++
  lcl|MicrobesOnline__882:209294 552 MIG 554
                                     *96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (563 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 7.36
//
[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:

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, 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

GapMind for Amino acid biosynthesis