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

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.18825.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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.02
# Mc/sec: 11.23
//
[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