Alignments for a candidate for ilvI in Desulfovibrio oxyclinae DSM 11498

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Desulfovibrio oxyclinae DSM 11498

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_018125050.1 B149_RS0109980 acetolactate synthase, large subunit, biosynthetic type

Query= SwissProt::P0DP90
         (548 letters)



>NCBI__GCF_000375485.1:WP_018125050.1
          Length = 559

 Score =  484 bits (1246), Expect = e-141
 Identities = 257/554 (46%), Positives = 352/554 (63%), Gaps = 12/554 (2%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDAL-YDGGVEHLLCRHEQGAAMAAIGYAR 59
           M GA+ ++  L  Q + TV G PGG  +P+YDAL     + H+L RHEQGAA  A G AR
Sbjct: 4   MTGAELLIRLLERQEITTVAGIPGGTNLPIYDALGRSSRIRHVLARHEQGAAFMAQGMAR 63

Query: 60  ATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSL 119
           +TGK  VC+ATSGPGATNL+T +ADA LDS+P+V ITGQV    +GTDAFQE+D+ G+S+
Sbjct: 64  STGKPAVCMATSGPGATNLLTAIADAKLDSVPIVCITGQVPLGLVGTDAFQEMDIYGMSI 123

Query: 120 ACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASG--DLEPWFTTVEN 177
             TKH++LV+S  EL  ++ EAF +A SGRPGPVLVDIPKDIQ  S   D+ P   T E 
Sbjct: 124 PVTKHNYLVRSARELLHVIPEAFRIAASGRPGPVLVDIPKDIQCQSVTFDMLPAPGTPE- 182

Query: 178 EVTFPHAEVEQ---ARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGL 234
             T P  +++Q   A +M+++++KP+LY+GGGV  + A            +P+  TL GL
Sbjct: 183 --TSPDPDIDQLNRAAEMISRSRKPILYLGGGVTQSGASETATRLAEKNTLPSVMTLMGL 240

Query: 235 GAVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMD 294
           GA+   +P  LGMLGMH  K  N A+QECDLLIA G RFDDR TG+L  F P A +IH+D
Sbjct: 241 GAMPHSHPLSLGMLGMHAAKHTNLALQECDLLIAAGVRFDDRATGRLEEFCPDADIIHID 300

Query: 295 IDPAEMNKLRQAHVALQGDLNALLPALQ---QPLNQYDWQQHCAQLRDEHSWRYDHPGDA 351
           IDP+E+ KL+   V +  D+   L  L    Q   + +W    A L+ +           
Sbjct: 301 IDPSELGKLKTDCVGIVCDVKTALEHLLANVQDKQRGEWVDRIATLKRDFPALLPKTASP 360

Query: 352 IYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAV 411
           +    L++  ++    D +VTTDVGQHQM AAQ    TR   F+TS GLGTMGFGLPAA+
Sbjct: 361 LSPYGLVRHAAEYVGPDAIVTTDVGQHQMRAAQAYPVTRARQFLTSGGLGTMGFGLPAAI 420

Query: 412 GAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQE 471
           GA +A P+ +V+C +GDGS +MN+QEL T     L +KIVL DN+ LG+V+Q Q+LF++ 
Sbjct: 421 GAALAHPDRSVICFTGDGSLLMNIQELATAAEHNLNIKIVLADNRALGLVQQQQELFYEN 480

Query: 472 RYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVW 531
           R   ++  +  DF  +A  FGI    +   +   + L  +L S+GP L+ + ++  ENV+
Sbjct: 481 RKFASSYGNALDFTTIAKGFGIASADLANSEDPASDLRDILGSNGPALIRIPVNAAENVY 540

Query: 532 PLVPPGASNSEMLE 545
           P+VPPGA+N+ M+E
Sbjct: 541 PMVPPGAANTTMIE 554


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: 815
Number of extensions: 39
Number of successful extensions: 4
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: 559
Length adjustment: 36
Effective length of query: 512
Effective length of database: 523
Effective search space:   267776
Effective search space used:   267776
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_018125050.1 B149_RS0109980 (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.13583.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.2e-208  679.2   0.0   2.5e-208  679.0   0.0    1.0  1  lcl|NCBI__GCF_000375485.1:WP_018125050.1  B149_RS0109980 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000375485.1:WP_018125050.1  B149_RS0109980 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  679.0   0.0  2.5e-208  2.5e-208       1     555 [.       4     554 ..       4     556 .. 0.98

  Alignments for each domain:
  == domain 1  score: 679.0 bits;  conditional E-value: 2.5e-208
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               ++gae+l++ l+++++ tv G+PGG+ lpiydal  +s ++h+l+rheq+aa +a+G+ar++Gk+ v++
  lcl|NCBI__GCF_000375485.1:WP_018125050.1   4 MTGAELLIRLLERQEITTVAGIPGGTNLPIYDALGrSSRIRHVLARHEQGAAFMAQGMARSTGKPAVCM 72 
                                               79********************************9899******************************* PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               atsGPGatnl+t+ia+a ldsvP+v +tGqv+  l+G+dafqe+di G+++pvtkh++lv++a++l ++
  lcl|NCBI__GCF_000375485.1:WP_018125050.1  73 ATSGPGATNLLTAIADAKLDSVPIVCITGQVPLGLVGTDAFQEMDIYGMSIPVTKHNYLVRSARELLHV 141
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206
                                               + eaf ia++GrPGPvlvd+Pkd++ +++++++      p   p   ++  q+++a+e+i++++kP+l+
  lcl|NCBI__GCF_000375485.1:WP_018125050.1 142 IPEAFRIAASGRPGPVLVDIPKDIQCQSVTFDMLPAPGTPETSP--DPDIDQLNRAAEMISRSRKPILY 208
                                               *****************************999986666565555..46778****************** PP

                                 TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275
                                                GgGv +++ase  ++lae+  +p ++tl+GlGa+p+ hpl+lgmlGmh +k++nla++e+dllia G+
  lcl|NCBI__GCF_000375485.1:WP_018125050.1 209 LGGGVTQSGASETATRLAEKNTLPSVMTLMGLGAMPHSHPLSLGMLGMHAAKHTNLALQECDLLIAAGV 277
                                               ********************************************************************* PP

                                 TIGR00118 276 rfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekie 344
                                               rfddr tg l++f+p+a iihididP+e+gk  +  + iv d+k+ le+ll++++++++ e  W+++i+
  lcl|NCBI__GCF_000375485.1:WP_018125050.1 278 RFDDRATGRLEEFCPDADIIHIDIDPSELGKLKTDCVGIVCDVKTALEHLLANVQDKQRGE--WVDRIA 344
                                               *******************************************************999998..****** PP

                                 TIGR00118 345 ewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmG 413
                                                +k++ +  l ++ +++ P  ++++  + +  +aivttdvGqhqm aaq y+++++r+f+tsgGlGtmG
  lcl|NCBI__GCF_000375485.1:WP_018125050.1 345 TLKRDFPALLPKTASPLSPYGLVRHAAEYVGPDAIVTTDVGQHQMRAAQAYPVTRARQFLTSGGLGTMG 413
                                               ********************************************************************* PP

                                 TIGR00118 414 fGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeery 482
                                               fGlPaa+Ga +a+p+ +v++ tGdgs+ mn+qel+t++e ++++kiv+ +n+ lG+v+q qelfye+r+
  lcl|NCBI__GCF_000375485.1:WP_018125050.1 414 FGLPAAIGAALAHPDRSVICFTGDGSLLMNIQELATAAEHNLNIKIVLADNRALGLVQQQQELFYENRK 482
                                               ********************************************************************* PP

                                 TIGR00118 483 setklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagld 551
                                                ++  ++   df+ +a+++G+ +  +++ e+ ++ l+++l s++p+l+ + v+  e+v+Pmv+pGa+++
  lcl|NCBI__GCF_000375485.1:WP_018125050.1 483 FASSYGN-ALDFTTIAKGFGIASADLANSEDPASDLRDILGSNGPALIRIPVNAAENVYPMVPPGAANT 550
                                               ******6.99*********************************************************** PP

                                 TIGR00118 552 elve 555
                                                ++e
  lcl|NCBI__GCF_000375485.1:WP_018125050.1 551 TMIE 554
                                               9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (559 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: 11.86
//
[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