GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Desulfovibrio vulgaris Hildenborough

Align Acetolactate synthase isozyme 2 large subunit; AHAS-II; ALS-II; Acetohydroxy-acid synthase II large subunit; EC 2.2.1.6 (characterized)
to candidate 209294 DVU0360 acetolactate synthase, large subunit, biosynthetic type

Query= SwissProt::P0DP90
         (548 letters)



>MicrobesOnline__882:209294
          Length = 563

 Score =  492 bits (1266), Expect = e-143
 Identities = 261/551 (47%), Positives = 354/551 (64%), Gaps = 8/551 (1%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDAL-YDGGVEHLLCRHEQGAAMAAIGYAR 59
           M+GA+ V+  L  QG++ + G PGGA +P+YDAL +   + H+L RHEQGA   A G AR
Sbjct: 4   MSGAELVIRLLERQGIDCISGIPGGANLPLYDALSHSKRIRHVLARHEQGAGFIAQGMAR 63

Query: 60  ATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSL 119
           +TG+  V  ATSGPGATN +T +ADA LDS+PV+ ITGQV    IG+DAFQEVD+ G+S+
Sbjct: 64  STGRPAVFFATSGPGATNTLTAIADAKLDSVPVICITGQVPRSMIGSDAFQEVDIYGMSI 123

Query: 120 ACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPW-FTTVENE 178
             TKH+FLV+S+E+L  ++ EAF +A SGRPGPVLVDIPKD+Q A    E W  T   + 
Sbjct: 124 PVTKHNFLVRSVEDLLTVIPEAFRIATSGRPGPVLVDIPKDVQTAEVAFEAWPETGGPDP 183

Query: 179 VTFPHAE-VEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAV 237
              P  E + +A +MLA+A++P+L++GGGV  + A    R F   T +P   +L GLG +
Sbjct: 184 AEAPDMEGLARAARMLAEAERPILFIGGGVVASGAGEVARVFAERTGLPTAMSLLGLGTL 243

Query: 238 EADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDP 297
             ++P  LGMLGMHG +  N  ++ECDLL+ VGARFDDR TG++  F PHAS+IH+DIDP
Sbjct: 244 PPEHPLTLGMLGMHGARCTNMLLEECDLLMVVGARFDDRATGRIEQFCPHASIIHVDIDP 303

Query: 298 AEMNKLRQAHVALQGD----LNALLPALQQPLNQYDWQQHCAQLRDEHSWRYDHPGDAIY 353
           +E++KLR AHVA+ GD    L ALLP L +P+++  W  H A+++  H        D   
Sbjct: 304 SEIDKLRTAHVAITGDAGRVLEALLPML-EPVDRKAWHGHVARMKAAHPLLTPGADDPRT 362

Query: 354 APLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVGA 413
              L+   +       ++ TDVGQHQM  AQ     R   ++TS GLGTMGFGLPAA+GA
Sbjct: 363 PYGLVTCTAACLDDSAIIATDVGQHQMRTAQAYPLRRTRQWLTSGGLGTMGFGLPAAIGA 422

Query: 414 QVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERY 473
            +A P  TVVC +GDGS  MN+QEL T       +KIVL +N  LG+V+Q Q LF+  R 
Sbjct: 423 ALANPERTVVCFTGDGSLQMNIQELATAAETGANVKIVLANNNALGLVQQQQDLFYGRRI 482

Query: 474 SETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVWPL 533
             +  T   DF+ +A  FG+    + R    +  L   L + GP L+HV +   ENV+P+
Sbjct: 483 FASDFTHRIDFVRIAEGFGVPAVDLGRSADPKRDLARALRAKGPCLIHVPVAVEENVYPM 542

Query: 534 VPPGASNSEML 544
           VPPGA+N+EM+
Sbjct: 543 VPPGAANTEMI 553


Lambda     K      H
   0.320    0.135    0.410 

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: 874
Number of extensions: 43
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: 548
Length of database: 563
Length adjustment: 36
Effective length of query: 512
Effective length of database: 527
Effective search space:   269824
Effective search space used:   269824
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.3288897.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 28.25
//
[ok]

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

Links

Downloads

Related tools

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:

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