Alignments for a candidate for ilvI in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Shewanella amazonensis SB2B

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 6939187 Sama_3281 acetolactate synthase 2 catalytic subunit (RefSeq)

Query= SwissProt::P0DP90
         (548 letters)



>FitnessBrowser__SB2B:6939187
          Length = 556

 Score =  729 bits (1883), Expect = 0.0
 Identities = 358/547 (65%), Positives = 434/547 (79%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARA 60
           M GA  V+  L A GVNTVFGYPGGAIMP+YDALY   VEH LCRHEQGA  AA+GYARA
Sbjct: 6   MRGADAVIKVLAAHGVNTVFGYPGGAIMPIYDALYGSEVEHTLCRHEQGAGFAAVGYARA 65

Query: 61  TGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLA 120
           +GKTGVC ATSGPGATNLIT LADALLDS+PVVAITGQVS   IGTDAFQE+DVLG+SL+
Sbjct: 66  SGKTGVCFATSGPGATNLITALADALLDSVPVVAITGQVSTSVIGTDAFQEIDVLGMSLS 125

Query: 121 CTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVT 180
           CTKHSF+VQ+++EL   +  AF++A SGRPGPVLVDIPKDIQ+A  +       V +E  
Sbjct: 126 CTKHSFMVQTVDELVPTLYRAFELAASGRPGPVLVDIPKDIQIAKLEYRAPLLAVADEPK 185

Query: 181 FPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEAD 240
              A+++ AR ++A A+KPMLYVGGGVGMA AV  LR F+ AT MP+  TLKGLGA+   
Sbjct: 186 VQDADIDAARALIAAAKKPMLYVGGGVGMAGAVEPLRHFIKATYMPSVATLKGLGAIPHG 245

Query: 241 YPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDPAEM 300
            P YLGMLGMHG KAAN AVQECDLL+ VGARFDDRVTG+L +FAP+A V+H+DID AE+
Sbjct: 246 TPGYLGMLGMHGGKAANLAVQECDLLMVVGARFDDRVTGRLASFAPNAKVLHLDIDAAEL 305

Query: 301 NKLRQAHVALQGDLNALLPALQQPLNQYDWQQHCAQLRDEHSWRYDHPGDAIYAPLLLKQ 360
            KLRQ  VA+  +L  +LP L+  L+   W+     L  EH W Y+HPG  IYAP +L++
Sbjct: 306 GKLRQPDVAIAAELRVVLPMLEMQLDIDPWRAEVEALAAEHRWDYNHPGSLIYAPAMLRR 365

Query: 361 LSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVGAQVARPND 420
           L+++ P D VV+ DVGQHQMW AQH+   RPE+ ++S+GLGTMGFGLPAA+GAQ+ARP+ 
Sbjct: 366 LANKLPEDSVVSCDVGQHQMWVAQHMHFRRPEDHLSSAGLGTMGFGLPAAIGAQMARPDA 425

Query: 421 TVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYSETTLTD 480
           TVV +SGDGSFMMNVQEL T+KR++LP+KI+L+DNQRLGMV+QWQQLFF+ERYSET L+D
Sbjct: 426 TVVAVSGDGSFMMNVQELTTIKRRKLPVKILLIDNQRLGMVKQWQQLFFEERYSETNLSD 485

Query: 481 NPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVWPLVPPGASN 540
           NPDF+ LASAF I G+ I   ++VE AL  ML S GPYLLHV+ID+  NVWPLVPPGASN
Sbjct: 486 NPDFVALASAFDIPGRTIFAAEEVEEALTEMLTSKGPYLLHVAIDDAFNVWPLVPPGASN 545

Query: 541 SEMLEKL 547
           S+M+E++
Sbjct: 546 SDMMEEM 552


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: 899
Number of extensions: 26
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: 556
Length adjustment: 36
Effective length of query: 512
Effective length of database: 520
Effective search space:   266240
Effective search space used:   266240
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 6939187 Sama_3281 (acetolactate synthase 2 catalytic subunit (RefSeq))
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.8064.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   5.5e-213  694.3   0.1   6.4e-213  694.1   0.1    1.0  1  lcl|FitnessBrowser__SB2B:6939187  Sama_3281 acetolactate synthase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6939187  Sama_3281 acetolactate synthase 2 catalytic subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  694.1   0.1  6.4e-213  6.4e-213       1     556 [.       6     551 ..       6     552 .. 0.97

  Alignments for each domain:
  == domain 1  score: 694.1 bits;  conditional E-value: 6.4e-213
                         TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlatsGPGatn 77 
                                       ++ga+++++ l ++gv+tvfGyPGGa++piydaly se+eh l rheq+a  aa GyarasGk+Gv++atsGPGatn
  lcl|FitnessBrowser__SB2B:6939187   6 MRGADAVIKVLAAHGVNTVFGYPGGAIMPIYDALYGSEVEHTLCRHEQGAGFAAVGYARASGKTGVCFATSGPGATN 82 
                                       79*************************************************************************** PP

                         TIGR00118  78 lvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPvl 154
                                       l+t++a+a ldsvP+v++tGqv+ts+iG+dafqeid+lG++l++tkhsf+v+ +++l  +l +afe+a++GrPGPvl
  lcl|FitnessBrowser__SB2B:6939187  83 LITALADALLDSVPVVAITGQVSTSVIGTDAFQEIDVLGMSLSCTKHSFMVQTVDELVPTLYRAFELAASGRPGPVL 159
                                       ***************************************************************************** PP

                         TIGR00118 155 vdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelkelaerlkipv 231
                                       vd+Pkd++ a++e++ +    l + + + k + + i +a  li++akkP+l+vGgGv +a+a e l+++ +++ +p 
  lcl|FitnessBrowser__SB2B:6939187 160 VDIPKDIQIAKLEYRAP----LLAVADEPKVQDADIDAARALIAAAKKPMLYVGGGVGMAGAVEPLRHFIKATYMPS 232
                                       ********999999887....555555556678899***************************************** PP

                         TIGR00118 232 tttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigknv 308
                                       ++tl GlGa+p+  p  lgmlGmhG k+anlav+e+dll+ vGarfddrvtg la+fap+ak++h+did ae+gk +
  lcl|FitnessBrowser__SB2B:6939187 233 VATLKGLGAIPHGTPGYLGMLGMHGGKAANLAVQECDLLMVVGARFDDRVTGRLASFAPNAKVLHLDIDAAELGKLR 309
                                       ***************************************************************************** PP

                         TIGR00118 309 kvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvG 385
                                       + d++i  + + vl  l  +l     +   W +++e + +e+   +++  + i   +++++l + l+++++v+ dvG
  lcl|FitnessBrowser__SB2B:6939187 310 QPDVAIAAELRVVLPMLEMQLD---ID--PWRAEVEALAAEHRWDYNHPGSLIYAPAMLRRLANKLPEDSVVSCDVG 381
                                       ************9987755442...22..3*************99**999999999********************* PP

                         TIGR00118 386 qhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivil 462
                                       qhqmw+aq+ ++++p+ +++s+GlGtmGfGlPaa+Ga++a p++tvvav+Gdgsf+mn+qel+ti++ ++pvki+++
  lcl|FitnessBrowser__SB2B:6939187 382 QHQMWVAQHMHFRRPEDHLSSAGLGTMGFGLPAAIGAQMARPDATVVAVSGDGSFMMNVQELTTIKRRKLPVKILLI 458
                                       ***************************************************************************** PP

                         TIGR00118 463 nnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeee 539
                                       +n+ lGmvkqWq+lf+eeryset+l+ ++pdfv+la a+ + g +i   ee+ee+l+e+l+sk+p+ll v +d+  +
  lcl|FitnessBrowser__SB2B:6939187 459 DNQRLGMVKQWQQLFFEERYSETNLS-DNPDFVALASAFDIPGRTIFAAEEVEEALTEMLTSKGPYLLHVAIDDAFN 534
                                       **************************.6************************************************* PP

                         TIGR00118 540 vlPmvapGagldelvee 556
                                       v+P+v+pGa++++++ee
  lcl|FitnessBrowser__SB2B:6939187 535 VWPLVPPGASNSDMMEE 551
                                       *************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (556 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: 00:00:00.02
# Mc/sec: 12.50
//
[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