Alignments for a candidate for ilvI in Desulfobacter vibrioformis DSM 8776

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Desulfobacter vibrioformis DSM 8776

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 WP_035235592.1 Q366_RS01295 acetolactate synthase, large subunit, biosynthetic type

Query= SwissProt::P0DP90
         (548 letters)



>NCBI__GCF_000745975.1:WP_035235592.1
          Length = 553

 Score =  487 bits (1253), Expect = e-142
 Identities = 260/560 (46%), Positives = 345/560 (61%), Gaps = 24/560 (4%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARA 60
           MNGAQ +V  L  QG+  ++G PGGA +P+YDALY   + H+L RHEQGA   A G AR 
Sbjct: 3   MNGAQLIVKLLERQGIKIIWGIPGGATLPLYDALYQSPIRHILTRHEQGAGFMAQGMART 62

Query: 61  TGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLA 120
           TGK  VC ATSGPGATNLIT LADA LDS+P+VAITGQV    +GTDAFQEVD  GL+L 
Sbjct: 63  TGKAAVCTATSGPGATNLITALADAHLDSVPMVAITGQVPTALMGTDAFQEVDTYGLTLP 122

Query: 121 CTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVT 180
            TKH+FLV++  +L  ++ EAF +A SGRPGPV+VD+PKD+Q        W    E  V 
Sbjct: 123 VTKHNFLVKAAADLLTVIPEAFRIAESGRPGPVVVDVPKDVQTQKVRFGQW---PEPGVP 179

Query: 181 FP-----HAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLG 235
            P     +  +E+  QM+ ++++PM YVGGGV  +     LR       +P   TL GLG
Sbjct: 180 GPVRWRDNGVLERMAQMIRQSKRPMFYVGGGVVASGGADLLRSASQKNGIPVVSTLMGLG 239

Query: 236 AVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDI 295
           A+  D P +LGMLGMHGT  AN A+   DL+IA+G RFDDRVTGK+  F   A+VIH+D+
Sbjct: 240 AMAYDDPLFLGMLGMHGTPVANLAMARADLIIALGIRFDDRVTGKMEAFCADAAVIHVDV 299

Query: 296 DPAEMNKLRQAHVALQGD----LNALLPALQQPLNQYDWQQHCAQLRDEHSWRYD----- 346
           D +E+ K+R A + + GD    L  +LP +     +  W    A L+       +     
Sbjct: 300 DESEIGKIRNASLGVCGDAATVLTKILPRM-DTFTREGWHGEIASLKSPTPAAAEIKNPF 358

Query: 347 HPGDAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFG 406
           HP        +++ + +R P D +V TDVGQHQMW AQ      P + + S GLGTMGFG
Sbjct: 359 HPSG------IIRYIGNRAPEDAIVATDVGQHQMWTAQAYPVRHPRSLLMSGGLGTMGFG 412

Query: 407 LPAAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQ 466
           +P A+GA  A P+  +VCI+GDGSF+MN+QEL T+   +L + IVL+DN  LG+VRQ Q+
Sbjct: 413 VPVAMGAAFANPHKKIVCITGDGSFLMNLQELATLAEHELNITIVLMDNGHLGLVRQQQE 472

Query: 467 LFFQERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDE 526
           +F+      +  T +PDF  +A  FGI            +A+D  L   GP L+ V ID 
Sbjct: 473 MFYSNHVFASKFTRSPDFSAIAQGFGIRAWDAGINGSNRSAIDEALAFQGPSLVVVPIDG 532

Query: 527 LENVWPLVPPGASNSEMLEK 546
             NV+P+VPPGASN EM+++
Sbjct: 533 TTNVYPMVPPGASNLEMIQE 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: 799
Number of extensions: 18
Number of successful extensions: 3
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: 553
Length adjustment: 36
Effective length of query: 512
Effective length of database: 517
Effective search space:   264704
Effective search space used:   264704
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 WP_035235592.1 Q366_RS01295 (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.5419.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.4e-207  673.9   0.3   9.5e-207  673.7   0.3    1.0  1  lcl|NCBI__GCF_000745975.1:WP_035235592.1  Q366_RS01295 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745975.1:WP_035235592.1  Q366_RS01295 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  673.7   0.3  9.5e-207  9.5e-207       1     556 [.       3     552 ..       3     553 .] 0.98

  Alignments for each domain:
  == domain 1  score: 673.7 bits;  conditional E-value: 9.5e-207
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               ++ga+++v+ l+++g+++++G+PGGa lp+ydaly+s ++hil+rheq+a  +a+G+ar++Gk+ v+ a
  lcl|NCBI__GCF_000745975.1:WP_035235592.1   3 MNGAQLIVKLLERQGIKIIWGIPGGATLPLYDALYQSPIRHILTRHEQGAGFMAQGMARTTGKAAVCTA 71 
                                               78******************************************************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatnl+t++a+a+ldsvP+v++tGqv+t+l+G+dafqe+d  G+tlpvtkh+flvk a+dl +++
  lcl|NCBI__GCF_000745975.1:WP_035235592.1  72 TSGPGATNLITALADAHLDSVPMVAITGQVPTALMGTDAFQEVDTYGLTLPVTKHNFLVKAAADLLTVI 140
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                                eaf ia++GrPGPv+vd+Pkdv+++++++ +  +  +pg  p    ++  +++ +++i+++k+P+ +v
  lcl|NCBI__GCF_000745975.1:WP_035235592.1 141 PEAFRIAESGRPGPVVVDVPKDVQTQKVRFGQWPEPGVPG--PVRWRDNGVLERMAQMIRQSKRPMFYV 207
                                               *******************************999999998..6677788899***************** PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgGv+++++ + l+  +++  ipv++tl+GlGa+  d+pl+lgmlGmhGt +anla+  adl+ia+G+r
  lcl|NCBI__GCF_000745975.1:WP_035235592.1 208 GGGVVASGGADLLRSASQKNGIPVVSTLMGLGAMAYDDPLFLGMLGMHGTPVANLAMARADLIIALGIR 276
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekiee 345
                                               fddrvtg+++ f+++a +ih+d+d +eigk++++ + + Gda +vl+++l ++ + +++   W  +i++
  lcl|NCBI__GCF_000745975.1:WP_035235592.1 277 FDDRVTGKMEAFCADAAVIHVDVDESEIGKIRNASLGVCGDAATVLTKILPRMDTFTREG--WHGEIAS 343
                                               *****************************************************9998887..******* PP

                                 TIGR00118 346 wkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGf 414
                                               +k+ ++ +  e +++++P  +i+ + + ++++aiv+tdvGqhqmw+aq y++++pr+ + sgGlGtmGf
  lcl|NCBI__GCF_000745975.1:WP_035235592.1 344 LKSPTPAA-AEIKNPFHPSGIIRYIGNRAPEDAIVATDVGQHQMWTAQAYPVRHPRSLLMSGGLGTMGF 411
                                               **999965.566789****************************************************** PP

                                 TIGR00118 415 GlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerys 483
                                               G+P a+Ga  a+p++++v++tGdgsf mnlqel+t++e ++++ iv+++n +lG+v+q qe+fy++   
  lcl|NCBI__GCF_000745975.1:WP_035235592.1 412 GVPVAMGAAFANPHKKIVCITGDGSFLMNLQELATLAEHELNITIVLMDNGHLGLVRQQQEMFYSNHVF 480
                                               ********************************************************************* PP

                                 TIGR00118 484 etklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGaglde 552
                                               ++k++  +pdf ++a+++G+++     +    ++++eal+ ++p l+ v +d +++v+Pmv+pGa++ e
  lcl|NCBI__GCF_000745975.1:WP_035235592.1 481 ASKFTR-SPDFSAIAQGFGIRAWDAGINGSNRSAIDEALAFQGPSLVVVPIDGTTNVYPMVPPGASNLE 548
                                               *****5.************************************************************** PP

                                 TIGR00118 553 lvee 556
                                               +++e
  lcl|NCBI__GCF_000745975.1:WP_035235592.1 549 MIQE 552
                                               *986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (553 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 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.12
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Protein sequences (fasta format)
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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