GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Dechlorosoma suillum PS

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 Dsui_1925 Dsui_1925 acetolactate synthase, large subunit, biosynthetic type

Query= SwissProt::P0DP90
         (548 letters)



>FitnessBrowser__PS:Dsui_1925
          Length = 572

 Score =  500 bits (1288), Expect = e-146
 Identities = 269/553 (48%), Positives = 350/553 (63%), Gaps = 12/553 (2%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGG-VEHLLCRHEQGAAMAAIGYAR 59
           + GAQ VV  L  QGV TV G PGGAI+P YDAL     + H+L RHEQGA   A G AR
Sbjct: 21  LTGAQIVVRLLERQGVTTVSGIPGGAILPFYDALSASEKIRHVLARHEQGAGFIAQGMAR 80

Query: 60  ATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSL 119
           A+G+  VC+A+SGPGATNL+T +ADA LDSIP+VAITGQV    IGTDAFQEVD  GLS+
Sbjct: 81  ASGQPAVCLASSGPGATNLLTAIADAKLDSIPLVAITGQVPRSMIGTDAFQEVDTYGLSI 140

Query: 120 ACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEV 179
             TKH+FLV S EEL  ++  AF +A SGRPGPVLVDIPKD+Q  + ++  W      + 
Sbjct: 141 PITKHNFLVNSAEELLEVIPRAFTLAASGRPGPVLVDIPKDVQAQAIEVSQWPAPGGRQA 200

Query: 180 --TFPHAEVEQARQMLAKAQKPMLYVGGGV---GMAQAVPALREFLAATKMPATCTLKGL 234
                 A +E+A  M+  A++P+LY+GGGV   G A+A  AL E      +P T TL  L
Sbjct: 201 PPAPDMAAIEKAAAMINAAERPILYLGGGVVHSGAAEAAVALAE---KASLPTTMTLMAL 257

Query: 235 GAVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMD 294
           GA+  D+P  + MLGMHG +  N  ++ECDLLIAVGARFDDR TGK+  F P A +IH+D
Sbjct: 258 GAMPVDHPLSIHMLGMHGARYTNLLLEECDLLIAVGARFDDRATGKVAAFCPKAQIIHID 317

Query: 295 IDPAEMNKLRQAHVALQGDLNALLPALQQPLNQY---DWQQHCAQLRDEHSWRYDHPGDA 351
           IDP+E++K++ AHV + GD+  +L  L   +  +    W  H   LR     +  +  D 
Sbjct: 318 IDPSELDKIKNAHVGIAGDVGEVLEKLSPLVEAHLRKRWLTHMGDLRSRFRLQRPNLEDP 377

Query: 352 IYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAV 411
                L++ ++D       + TDVGQHQMW AQ     RP  ++TS GLGTMGFG+PAA+
Sbjct: 378 RSHYGLIQAVADCLDDSAAIATDVGQHQMWVAQAYPLRRPRQWLTSGGLGTMGFGVPAAL 437

Query: 412 GAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQE 471
           GA +A P  TVVC +GDGS +MN+QEL T+      LKIVL++N  LG+V Q Q+LF+ +
Sbjct: 438 GAALAEPERTVVCFTGDGSILMNIQELATIAEAGANLKIVLMNNDALGLVYQQQELFYGK 497

Query: 472 RYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVW 531
           RY  +     PDFL +A  FGI    +       AAL   L   GP L+H  ID  E V+
Sbjct: 498 RYFASKFAGQPDFLKIAEGFGIDTLDLDTAADPRAALRQALQRPGPCLIHAFIDMNEKVY 557

Query: 532 PLVPPGASNSEML 544
           P+VPPGA+N++M+
Sbjct: 558 PMVPPGAANTDMI 570


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: 842
Number of extensions: 28
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: 572
Length adjustment: 36
Effective length of query: 512
Effective length of database: 536
Effective search space:   274432
Effective search space used:   274432
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 Dsui_1925 Dsui_1925 (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.22738.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.8e-210  685.4   0.0   3.1e-210  685.2   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_1925  Dsui_1925 acetolactate synthase,


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_1925  Dsui_1925 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  685.2   0.0  3.1e-210  3.1e-210       1     555 [.      21     571 ..      21     572 .] 0.98

  Alignments for each domain:
  == domain 1  score: 685.2 bits;  conditional E-value: 3.1e-210
                         TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPGat 76 
                                       l+ga+i+v+ l+++gv tv G+PGGa+lp+ydal  +++++h+l+rheq+a  +a+G+arasG++ v+la sGPGat
  lcl|FitnessBrowser__PS:Dsui_1925  21 LTGAQIVVRLLERQGVTTVSGIPGGAILPFYDALSaSEKIRHVLARHEQGAGFIAQGMARASGQPAVCLASSGPGAT 97 
                                       68*********************************8899************************************** PP

                         TIGR00118  77 nlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPv 153
                                       nl+t+ia+a lds+Plv++tGqv++s+iG+dafqe+d  G+++p+tkh+flv++ae+l e++ +af++a++GrPGPv
  lcl|FitnessBrowser__PS:Dsui_1925  98 NLLTAIADAKLDSIPLVAITGQVPRSMIGTDAFQEVDTYGLSIPITKHNFLVNSAEELLEVIPRAFTLAASGRPGPV 174
                                       ***************************************************************************** PP

                         TIGR00118 154 lvdlPkdvteaeieleveekvelp.gykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlki 229
                                       lvd+Pkdv++++ie+++      p g +    ++ + i+ka+ +i++a++P+l+ GgGv++++a e  + lae++ +
  lcl|FitnessBrowser__PS:Dsui_1925 175 LVDIPKDVQAQAIEVSQW---PAPgGRQAPPAPDMAAIEKAAAMINAAERPILYLGGGVVHSGAAEAAVALAEKASL 248
                                       ************998876...4441555667889999**************************************** PP

                         TIGR00118 230 pvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigk 306
                                       p t+tl+ lGa+p dhpl++ mlGmhG++++nl ++e+dlliavGarfddr tg++a f+p+a+iihididP+e++k
  lcl|FitnessBrowser__PS:Dsui_1925 249 PTTMTLMALGAMPVDHPLSIHMLGMHGARYTNLLLEECDLLIAVGARFDDRATGKVAAFCPKAQIIHIDIDPSELDK 325
                                       ***************************************************************************** PP

                         TIGR00118 307 nvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttd 383
                                       + ++++ i Gd+ +vle+l   ++++ +k   Wl ++ +++++  l+  + e++     +i+++   l+d+a ++td
  lcl|FitnessBrowser__PS:Dsui_1925 326 IKNAHVGIAGDVGEVLEKLSPLVEAHLRKR--WLTHMGDLRSRFRLQRPNLEDPRSHYGLIQAVADCLDDSAAIATD 400
                                       *******************99998877666..********************************************* PP

                         TIGR00118 384 vGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkiv 460
                                       vGqhqmw+aq y+ ++pr+++tsgGlGtmGfG+PaalGa +a+pe tvv+ tGdgs+ mn+qel+ti+e++ ++kiv
  lcl|FitnessBrowser__PS:Dsui_1925 401 VGQHQMWVAQAYPLRRPRQWLTSGGLGTMGFGVPAALGAALAEPERTVVCFTGDGSILMNIQELATIAEAGANLKIV 477
                                       ***************************************************************************** PP

                         TIGR00118 461 ilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdke 537
                                       ++nn+ lG+v+q qelfy +ry ++k+a ++pdf k+ae++G+ ++ + + ++  ++l++al+  +p l+   +d +
  lcl|FitnessBrowser__PS:Dsui_1925 478 LMNNDALGLVYQQQELFYGKRYFASKFA-GQPDFLKIAEGFGIDTLDLDTAADPRAALRQALQRPGPCLIHAFIDMN 553
                                       ****************************.6*********************************************** PP

                         TIGR00118 538 eevlPmvapGagldelve 555
                                       e+v+Pmv+pGa+++++++
  lcl|FitnessBrowser__PS:Dsui_1925 554 EKVYPMVPPGAANTDMIG 571
                                       ***************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (572 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 0.00s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.96
//
[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