Alignments for a candidate for ilvI in Sulfurimonas denitrificans DSM 1251

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Sulfurimonas denitrificans DSM 1251

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_011372771.1 SUDEN_RS05980 acetolactate synthase, large subunit, biosynthetic type

Query= metacyc::MONOMER-18810
         (585 letters)



>NCBI__GCF_000012965.1:WP_011372771.1
          Length = 565

 Score =  571 bits (1471), Expect = e-167
 Identities = 288/563 (51%), Positives = 387/563 (68%), Gaps = 6/563 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           ++ GA+I++ AL  EGV+ V+GYPGGA++ +YDE++KQ  F+HIL RHEQAAVHAA+GY+
Sbjct: 2   QISGAQIVIEALIAEGVDTVFGYPGGAIMNVYDEIYKQNNFKHILTRHEQAAVHAAEGYS 61

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           +A+GKVGVA++TSGPG TNAVTG+A AY+DSIP+VVI+G VP   IG DAFQE D VGI+
Sbjct: 62  KASGKVGVAMITSGPGFTNAVTGLADAYMDSIPLVVISGQVPMSLIGTDAFQEIDAVGIS 121

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           R   KHN+LV D +DLA  +K+AF+IA++GRPGPV VDIPKDV+    +++Y   +D+ +
Sbjct: 122 RSCTKHNYLVTDAKDLARVLKEAFYIASSGRPGPVHVDIPKDVTAQLAEFDYSIELDLET 181

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           Y P  KG+  QI+KA+  +  A RP  Y GGG++ +NA+ E+R+L   TG P   T M  
Sbjct: 182 YKPHTKGNPRQIKKAMEAISKARRPIFYLGGGIINSNAAYEVRELVKKTGIPAVETFMAR 241

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           G      +  + MLGMHG+Y ANMAM   D++I +GARFDDRV G  + F   A  +IH+
Sbjct: 242 GTLSHDDELLISMLGMHGSYAANMAMSETDLVIGLGARFDDRVTGKLSEFAKNA-GVIHV 300

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCL 377
           DIDP+SISK V  D PIVG+VK+V+ E+I    +S I P +   A W E I  +  +  L
Sbjct: 301 DIDPASISKLVIADYPIVGDVKNVVNEMIE--LSSSINPAK--YASWRETIRNFDELHPL 356

Query: 378 KYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437
            Y   ++ +KPQ+V++++ EL    A I +DVGQHQMW+AQFY F  PR++I+SGGLGTM
Sbjct: 357 TYHEDTDRLKPQWVIQRVGELLGDSANISTDVGQHQMWSAQFYPFTRPRQFISSGGLGTM 416

Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497
           G G P AMG+K A P+K  +  TG+GSI M  QEL T ++   PV    LNN YLGMVRQ
Sbjct: 417 GFGFPAAMGVKVASPDKISINFTGDGSILMNCQELMTAVEKKLPVINIILNNNYLGMVRQ 476

Query: 498 WQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDF 557
           WQ + YD R+S + +   PDFVKLAEA+G +G RV    + + AL+EA   K+   F+D 
Sbjct: 477 WQTLFYDKRHSETDLSVQPDFVKLAEAFGGIGFRVTTKEEFDAALKEAVE-KNIVTFIDV 535

Query: 558 QTDPTENVWPMVQAGKGISEMLL 580
             +  ENV PMV AG  +  M+L
Sbjct: 536 VVERLENVMPMVPAGGSLFNMML 558


Lambda     K      H
   0.319    0.135    0.407 

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: 845
Number of extensions: 29
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: 585
Length of database: 565
Length adjustment: 36
Effective length of query: 549
Effective length of database: 529
Effective search space:   290421
Effective search space used:   290421
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_011372771.1 SUDEN_RS05980 (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.31587.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.6e-245  799.7   1.2   8.1e-245  799.4   1.2    1.0  1  lcl|NCBI__GCF_000012965.1:WP_011372771.1  SUDEN_RS05980 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000012965.1:WP_011372771.1  SUDEN_RS05980 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  799.4   1.2  8.1e-245  8.1e-245       2     555 ..       4     558 ..       3     560 .. 0.99

  Alignments for each domain:
  == domain 1  score: 799.4 bits;  conditional E-value: 8.1e-245
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               +ga+i++e+l +egv+tvfGyPGGa++++yd++y +++++hil+rheqaa+haa+Gy++asGkvGv++ 
  lcl|NCBI__GCF_000012965.1:WP_011372771.1   4 SGAQIVIEALIAEGVDTVFGYPGGAIMNVYDEIYkQNNFKHILTRHEQAAVHAAEGYSKASGKVGVAMI 72 
                                               89********************************999******************************** PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPG tn+vtg+a+ay+ds+Plvv++Gqv+ sliG+dafqeid +Gi++++tkh++lv++a+dl+++l
  lcl|NCBI__GCF_000012965.1:WP_011372771.1  73 TSGPGFTNAVTGLADAYMDSIPLVVISGQVPMSLIGTDAFQEIDAVGISRSCTKHNYLVTDAKDLARVL 141
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               keaf+ias+GrPGPv+vd+Pkdvt++  e++++ +++l +ykp++kg+++qikka+e+i+ka++P+ + 
  lcl|NCBI__GCF_000012965.1:WP_011372771.1 142 KEAFYIASSGRPGPVHVDIPKDVTAQLAEFDYSIELDLETYKPHTKGNPRQIKKAMEAISKARRPIFYL 210
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgG+i ++a  e++el++++ ip + t++  G++ +d++l + mlGmhG+++an+a+se+dl+i++Gar
  lcl|NCBI__GCF_000012965.1:WP_011372771.1 211 GGGIINSNAAYEVRELVKKTGIPAVETFMARGTLSHDDELLISMLGMHGSYAANMAMSETDLVIGLGAR 279
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkeke.Wlekie 344
                                               fddrvtg+l++fa++a +ih+didPa+i+k v +d pivGd+k+v++e+++  ++ +  +   W e i+
  lcl|NCBI__GCF_000012965.1:WP_011372771.1 280 FDDRVTGKLSEFAKNAGVIHVDIDPASISKLVIADYPIVGDVKNVVNEMIELSSSINPAKYAsWRETIR 348
                                               ****************************************************99997666656****** PP

                                 TIGR00118 345 ewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmG 413
                                               ++ + ++l+++e+ + +kPq vi+++ +ll d+a ++tdvGqhqmw+aqfy++++pr+fi+sgGlGtmG
  lcl|NCBI__GCF_000012965.1:WP_011372771.1 349 NFDELHPLTYHEDTDRLKPQWVIQRVGELLGDSANISTDVGQHQMWSAQFYPFTRPRQFISSGGLGTMG 417
                                               ********************************************************************* PP

                                 TIGR00118 414 fGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeery 482
                                               fG+Paa+G+kva p++  ++ tGdgs+ mn+qel t+ve ++pv+ +ilnn++lGmv+qWq lfy++r+
  lcl|NCBI__GCF_000012965.1:WP_011372771.1 418 FGFPAAMGVKVASPDKISINFTGDGSILMNCQELMTAVEKKLPVINIILNNNYLGMVRQWQTLFYDKRH 486
                                               ********************************************************************* PP

                                 TIGR00118 483 setklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagld 551
                                               set l+  +pdfvklaea+G  g r++++ee +++lkea+e++   ++dv+v++ e+v+Pmv+ G++l 
  lcl|NCBI__GCF_000012965.1:WP_011372771.1 487 SETDLSV-QPDFVKLAEAFGGIGFRVTTKEEFDAALKEAVEKNIVTFIDVVVERLENVMPMVPAGGSLF 554
                                               ******6.************************************************************9 PP

                                 TIGR00118 552 elve 555
                                               +++ 
  lcl|NCBI__GCF_000012965.1:WP_011372771.1 555 NMML 558
                                               9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (565 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: 00:00:00.03
# Mc/sec: 7.89
//
[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