Alignments for a candidate for ilvI in Desulfobulbus mediterraneus DSM 13871

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Desulfobulbus mediterraneus DSM 13871

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_028583815.1 G494_RS0106080 acetolactate synthase, large subunit, biosynthetic type

Query= SwissProt::P0DP90
         (548 letters)



>NCBI__GCF_000429965.1:WP_028583815.1
          Length = 560

 Score =  484 bits (1246), Expect = e-141
 Identities = 257/554 (46%), Positives = 351/554 (63%), Gaps = 14/554 (2%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGV-EHLLCRHEQGAAMAAIGYAR 59
           + GA   +  L   G+ T+ G PGGA +P+Y+AL    V  H+L RHEQGA   A G AR
Sbjct: 4   LTGATLTIRLLEHYGITTIAGIPGGANLPLYEALSQSSVIRHVLARHEQGAGFMAQGMAR 63

Query: 60  ATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSL 119
           ++G+  VC ATSGPGATN++T +ADA LDSIPV+ ITGQV    IGTDAFQEVD+ GL++
Sbjct: 64  SSGRPAVCFATSGPGATNILTAIADAYLDSIPVICITGQVPQDLIGTDAFQEVDIYGLTI 123

Query: 120 ACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLE--PWFTTVEN 177
             TKH++LV+S EEL +++ EAF +A SGRPGPV++DIPKD+QL +  +   P    +  
Sbjct: 124 PITKHNYLVRSGEELLKVIPEAFAIASSGRPGPVVIDIPKDVQLETVQVAGLPEIPALAA 183

Query: 178 EVTFPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAV 237
            V  P   + QA  ++ +A+ P+LY+GGGV  + A    R     +++P T TL GLG +
Sbjct: 184 PVQVPAESLHQAASLINQAKAPVLYLGGGVVHSGAGLLARRLAERSQLPTTMTLMGLGII 243

Query: 238 EADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDP 297
             ++  Y+GMLGMH  ++ N  + ECDLLIA G RFDDR TGK+  F P A +IH+DIDP
Sbjct: 244 PPEHELYMGMLGMHAARSTNIMLDECDLLIAAGVRFDDRATGKIAEFCPDARIIHLDIDP 303

Query: 298 AEMNKLRQAHVALQGD----LNALLPAL---QQPLNQYDWQQHCAQLRDEHSWRYDHPGD 350
           +E++KL+QAH+ L GD    L  LLP +   ++PL    WQQ   QLR  H +      D
Sbjct: 304 SEISKLKQAHLGLVGDIAQTLERLLPLVSRRERPL----WQQRVRQLRAAHPFFCAEELD 359

Query: 351 AIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAA 410
                 ++ ++++      +V TDVG+HQMW AQ     RP  F+TS GLGTMGFGLP A
Sbjct: 360 FSRPYGIILRIAEIIGDQALVATDVGKHQMWTAQIYPLQRPRQFLTSGGLGTMGFGLPTA 419

Query: 411 VGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQ 470
           +GA +  P+  VVCISGDGS MMN+QEL T   + L LK+V+L+NQ LG+VRQ Q+LF+ 
Sbjct: 420 IGAALQHPDKPVVCISGDGSIMMNIQELATAVEQDLNLKVVVLNNQSLGLVRQQQKLFYG 479

Query: 471 ERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENV 530
            R   +    NPD   +A  FG+      +    +  L   L + GP L+++ ID  E V
Sbjct: 480 GRIFASEYRHNPDLAAIARGFGMKAFDCGQTLLFDEVLAVALQTPGPCLINIPIDIDEEV 539

Query: 531 WPLVPPGASNSEML 544
           +P+VPPGA+NS M+
Sbjct: 540 YPMVPPGAANSVMI 553


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: 822
Number of extensions: 33
Number of successful extensions: 5
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: 560
Length adjustment: 36
Effective length of query: 512
Effective length of database: 524
Effective search space:   268288
Effective search space used:   268288
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_028583815.1 G494_RS0106080 (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.12994.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.2e-204  665.4   0.0   3.6e-204  665.2   0.0    1.0  1  lcl|NCBI__GCF_000429965.1:WP_028583815.1  G494_RS0106080 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429965.1:WP_028583815.1  G494_RS0106080 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  665.2   0.0  3.6e-204  3.6e-204       1     556 [.       4     555 ..       4     556 .. 0.98

  Alignments for each domain:
  == domain 1  score: 665.2 bits;  conditional E-value: 3.6e-204
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               l+ga++ ++ l++ g+ t+ G+PGGa lp+y+al  +s ++h+l+rheq+a  +a+G+ar+sG++ v++
  lcl|NCBI__GCF_000429965.1:WP_028583815.1   4 LTGATLTIRLLEHYGITTIAGIPGGANLPLYEALSqSSVIRHVLARHEQGAGFMAQGMARSSGRPAVCF 72 
                                               689*******************************978889***************************** PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               atsGPGatn++t+ia+aylds+P++ +tGqv+++liG+dafqe+di G+t+p+tkh++lv++ e+l ++
  lcl|NCBI__GCF_000429965.1:WP_028583815.1  73 ATSGPGATNILTAIADAYLDSIPVICITGQVPQDLIGTDAFQEVDIYGLTIPITKHNYLVRSGEELLKV 141
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206
                                               + eaf ias+GrPGPv++d+Pkdv+ +++++      e+p+ +  v+     +++a+ li++ak Pvl+
  lcl|NCBI__GCF_000429965.1:WP_028583815.1 142 IPEAFAIASSGRPGPVVIDIPKDVQLETVQVAGL--PEIPALAAPVQVPAESLHQAASLINQAKAPVLY 208
                                               **************************99988766..689999999999999****************** PP

                                 TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275
                                                GgGv++++a    ++laer ++p t+tl+GlG +p +h+l +gmlGmh ++ +n+ ++e+dllia G+
  lcl|NCBI__GCF_000429965.1:WP_028583815.1 209 LGGGVVHSGAGLLARRLAERSQLPTTMTLMGLGIIPPEHELYMGMLGMHAARSTNIMLDECDLLIAAGV 277
                                               ********************************************************************* PP

                                 TIGR00118 276 rfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekie 344
                                               rfddr tg++a+f+p+a+iih+didP+ei+k  ++++ +vGd  + le+ll  ++++e+    W ++++
  lcl|NCBI__GCF_000429965.1:WP_028583815.1 278 RFDDRATGKIAEFCPDARIIHLDIDPSEISKLKQAHLGLVGDIAQTLERLLPLVSRRERPL--WQQRVR 344
                                               *****************************************************99988777..****** PP

                                 TIGR00118 345 ewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmG 413
                                               ++++ +++   ee +  +P  +i ++ +++ d+a+v+tdvG+hqmw+aq y+ ++pr+f+tsgGlGtmG
  lcl|NCBI__GCF_000429965.1:WP_028583815.1 345 QLRAAHPFFCAEELDFSRPYGIILRIAEIIGDQALVATDVGKHQMWTAQIYPLQRPRQFLTSGGLGTMG 413
                                               ********************************************************************* PP

                                 TIGR00118 414 fGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeery 482
                                               fGlP+a+Ga + +p++ vv+++Gdgs++mn+qel+t+ve d+++k+v+lnn+ lG+v+q q+lfy +r 
  lcl|NCBI__GCF_000429965.1:WP_028583815.1 414 FGLPTAIGAALQHPDKPVVCISGDGSIMMNIQELATAVEQDLNLKVVVLNNQSLGLVRQQQKLFYGGRI 482
                                               ********************************************************************* PP

                                 TIGR00118 483 setklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagld 551
                                                +++   ++pd++++a+++G+k+    +    +e l+ al++ +p l+++ +d +eev+Pmv+pGa+++
  lcl|NCBI__GCF_000429965.1:WP_028583815.1 483 FASEYR-HNPDLAAIARGFGMKAFDCGQTLLFDEVLAVALQTPGPCLINIPIDIDEEVYPMVPPGAANS 550
                                               *****9.59***********************************************************9 PP

                                 TIGR00118 552 elvee 556
                                                +++e
  lcl|NCBI__GCF_000429965.1:WP_028583815.1 551 VMIGE 555
                                               99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (560 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.81
//
[ok]

This GapMind analysis is from Apr 10 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