GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Shewanella oneidensis MR-1

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 203425 SO4347 acetolactate synthase II, large subunit (NCBI ptt file)

Query= SwissProt::P0DP90
         (548 letters)



>FitnessBrowser__MR1:203425
          Length = 552

 Score =  714 bits (1844), Expect = 0.0
 Identities = 353/547 (64%), Positives = 426/547 (77%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARA 60
           + GA  V+  L A GV TVFGYPGGAIMP+YDALY   VEHLL RHEQGAA AA+GYARA
Sbjct: 2   IRGADAVIKVLAAHGVTTVFGYPGGAIMPIYDALYGSPVEHLLSRHEQGAAFAAVGYARA 61

Query: 61  TGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLA 120
           +GKTGVC ATSGPGATNLIT LADALLDS+PVVAITGQVS   IGTDAFQE+DVLG+SL+
Sbjct: 62  SGKTGVCFATSGPGATNLITSLADALLDSVPVVAITGQVSTAVIGTDAFQEIDVLGMSLS 121

Query: 121 CTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVT 180
           CTKHSF+V  + +L   + +AF++A SGRPGPVLVDIPKDIQ+A  +       V NE  
Sbjct: 122 CTKHSFMVTDVNDLIPTLYQAFEIAASGRPGPVLVDIPKDIQIAHLEYRTPLLAVTNEPQ 181

Query: 181 FPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEAD 240
              +++  AR +LA+A++PMLYVGGGVGMA AV  LR+F+  T MP+  TLKGLG++   
Sbjct: 182 AEMSDINAARALLAQAKQPMLYVGGGVGMAGAVDQLRDFINTTGMPSVATLKGLGSIAHG 241

Query: 241 YPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDPAEM 300
            P YLGMLGMHG KAAN AVQ+CDLL+  GARFDDRVTG+L TFA  A VIH+DID AE+
Sbjct: 242 TPGYLGMLGMHGGKAANLAVQDCDLLVVAGARFDDRVTGRLATFANKAKVIHLDIDAAEL 301

Query: 301 NKLRQAHVALQGDLNALLPALQQPLNQYDWQQHCAQLRDEHSWRYDHPGDAIYAPLLLKQ 360
            KLRQ  VA+ GDL  + PAL   LN   WQ     L  +H W Y HPG  IYAP +L++
Sbjct: 302 GKLRQPDVAIAGDLRQIFPALAMSLNITPWQVEVEHLARKHQWDYQHPGSLIYAPAMLRR 361

Query: 361 LSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVGAQVARPND 420
           L+++ P D VV  DVGQHQMW AQH+   RPE+ ++S+GLGTMGFGLPAA+GAQVARP+ 
Sbjct: 362 LANKLPEDSVVCCDVGQHQMWVAQHMWFRRPEDHLSSAGLGTMGFGLPAAIGAQVARPDA 421

Query: 421 TVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYSETTLTD 480
           TVV +SGDGSFMMNVQEL T+KR++LP+KI+L+DNQ+LGMV+QWQQLFF+ RYSET L+D
Sbjct: 422 TVVTVSGDGSFMMNVQELTTIKRRKLPVKILLIDNQKLGMVKQWQQLFFEGRYSETDLSD 481

Query: 481 NPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVWPLVPPGASN 540
           NPDF+ LASAF I G+ I   D+VE AL  ML + GPYLLHV+ID+  NVWPLVPPGASN
Sbjct: 482 NPDFVQLASAFDIPGRTIFSSDEVEEALTEMLAAKGPYLLHVAIDDAFNVWPLVPPGASN 541

Query: 541 SEMLEKL 547
           S+M++++
Sbjct: 542 SDMMDEM 548


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: 924
Number of extensions: 30
Number of successful extensions: 1
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: 552
Length adjustment: 36
Effective length of query: 512
Effective length of database: 516
Effective search space:   264192
Effective search space used:   264192
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 203425 SO4347 (acetolactate synthase II, large subunit (NCBI ptt file))
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.3639912.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.6e-211  689.5   0.2   1.9e-211  689.3   0.2    1.0  1  lcl|FitnessBrowser__MR1:203425  SO4347 acetolactate synthase II,


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:203425  SO4347 acetolactate synthase II, large subunit (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  689.3   0.2  1.9e-211  1.9e-211       2     556 ..       3     547 ..       2     548 .. 0.97

  Alignments for each domain:
  == domain 1  score: 689.3 bits;  conditional E-value: 1.9e-211
                       TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlatsGPGatnlvt 80 
                                     +ga+++++ l ++gv tvfGyPGGa++piydaly s +eh+l rheq+aa aa GyarasGk+Gv++atsGPGatnl+t
  lcl|FitnessBrowser__MR1:203425   3 RGADAVIKVLAAHGVTTVFGYPGGAIMPIYDALYGSPVEHLLSRHEQGAAFAAVGYARASGKTGVCFATSGPGATNLIT 81 
                                     79***************************************************************************** PP

                       TIGR00118  81 giatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPvlvdlPk 159
                                     ++a+a ldsvP+v++tGqv+t++iG+dafqeid+lG++l++tkhsf+v++++dl  +l +afeia++GrPGPvlvd+Pk
  lcl|FitnessBrowser__MR1:203425  82 SLADALLDSVPVVAITGQVSTAVIGTDAFQEIDVLGMSLSCTKHSFMVTDVNDLIPTLYQAFEIAASGRPGPVLVDIPK 160
                                     ******************************************************************************* PP

                       TIGR00118 160 dvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlkipvtttllGl 238
                                     d++ a++e++++    l +   + +++   i++a  l+++ak+P+l+vGgGv +a+a ++l+++ +++ +p ++tl Gl
  lcl|FitnessBrowser__MR1:203425 161 DIQIAHLEYRTP----LLAVTNEPQAEMSDINAARALLAQAKQPMLYVGGGVGMAGAVDQLRDFINTTGMPSVATLKGL 235
                                     ****99999877....55666666778899************************************************* PP

                       TIGR00118 239 GafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGd 317
                                     G++ +  p  lgmlGmhG k+anlav+++dll+  Garfddrvtg la+fa++ak+ih+did ae+gk ++ d++i Gd
  lcl|FitnessBrowser__MR1:203425 236 GSIAHGTPGYLGMLGMHGGKAANLAVQDCDLLVVAGARFDDRVTGRLATFANKAKVIHLDIDAAELGKLRQPDVAIAGD 314
                                     ******************************************************************************* PP

                       TIGR00118 318 akkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyk 396
                                      ++++  l   l+    +   W  ++e++ +++   +++  + i   +++++l + l+++++v  dvGqhqmw+aq+  
  lcl|FitnessBrowser__MR1:203425 315 LRQIFPALAMSLNI---T--PWQVEVEHLARKHQWDYQHPGSLIYAPAMLRRLANKLPEDSVVCCDVGQHQMWVAQHMW 388
                                     99999988766643...3..4999*****9999999999999999999******************************* PP

                       TIGR00118 397 tkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqe 475
                                     +++p+ +++s+GlGtmGfGlPaa+Ga+va p++tvv+v+Gdgsf+mn+qel+ti++ ++pvki++++n+ lGmvkqWq+
  lcl|FitnessBrowser__MR1:203425 389 FRRPEDHLSSAGLGTMGFGLPAAIGAQVARPDATVVTVSGDGSFMMNVQELTTIKRRKLPVKILLIDNQKLGMVKQWQQ 467
                                     ******************************************************************************* PP

                       TIGR00118 476 lfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelv 554
                                     lf+e+ryset l+ ++pdfv+la a+ + g +i + +e+ee+l+e+l+ k+p+ll v +d+  +v+P+v+pGa++++++
  lcl|FitnessBrowser__MR1:203425 468 LFFEGRYSETDLS-DNPDFVQLASAFDIPGRTIFSSDEVEEALTEMLAAKGPYLLHVAIDDAFNVWPLVPPGASNSDMM 545
                                     *************.6**************************************************************99 PP

                       TIGR00118 555 ee 556
                                     +e
  lcl|FitnessBrowser__MR1:203425 546 DE 547
                                     75 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (552 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 27.01
//
[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:

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