Alignments for a candidate for ilvI in Nitratiruptor tergarcus DSM 16512

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Nitratiruptor tergarcus DSM 16512

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_084275805.1 B8779_RS06920 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_900176045.1:WP_084275805.1
          Length = 564

 Score =  587 bits (1514), Expect = e-172
 Identities = 298/567 (52%), Positives = 390/567 (68%), Gaps = 5/567 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           +M GA+++V A+ EEGVE V+GYPGGA++ +YDE++K   FEHIL RHEQAAVHAADGYA
Sbjct: 3   QMSGAQMVVEAMREEGVEVVFGYPGGAIMNVYDEIYKHRYFEHILTRHEQAAVHAADGYA 62

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           RATGKVGVA VTSGPG TNAVTG+ATAY+DSIP+VV++G VP   IG DAFQE D VGI+
Sbjct: 63  RATGKVGVAFVTSGPGFTNAVTGLATAYMDSIPLVVVSGQVPLSMIGTDAFQEIDAVGIS 122

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP  KHN+LVK   +L   + +AF+IA +GRPGPV VDIPKDV+    ++ YPK I + +
Sbjct: 123 RPCTKHNYLVKSAEELPHILAEAFYIARSGRPGPVHVDIPKDVTAQIAEFNYPKEIKLET 182

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           Y P  KG++ QI+KA+  +  A++P  Y GGG++ +N++D +R+L   T  P   TLM  
Sbjct: 183 YKPTIKGNARQIKKAIEAIAQAKKPVFYLGGGIIHSNSADLVRELVQATQIPAVETLMAR 242

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           G      +  +GM+GMHGTY ANMAM   D+LIA+G RFDDRV G  + F   A +IIH+
Sbjct: 243 GTLRYDDELLLGMVGMHGTYAANMAMSEADLLIALGPRFDDRVTGKLSEFAKYA-QIIHV 301

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCL 377
           DIDPSSI K V VD PIVG++K VL+E++ Q K   + P R     W + + ++  +  L
Sbjct: 302 DIDPSSIGKLVHVDYPIVGDLKKVLEEMVPQAK-EKVDPSR--YEPWRDILRRYNELHPL 358

Query: 378 KYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437
            Y+ S E++KP++V++++ E  KG A I +DVGQHQMW AQFY F  PR +I SGGLGTM
Sbjct: 359 TYEDSDEVLKPEWVIQRVGEKLKGKARISTDVGQHQMWTAQFYPFTRPREFITSGGLGTM 418

Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497
           G G P AMG+KK  P++  V I+G+GSI M IQEL T ++Y  PV    LNN YLGMVRQ
Sbjct: 419 GFGFPAAMGVKKGIPDEISVNISGDGSILMNIQELMTAVEYRLPVINIILNNNYLGMVRQ 478

Query: 498 WQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDF 557
           WQ   YD RY+ + +   PDFV+LAE++G VG RV+   + + AL +A   K     +D 
Sbjct: 479 WQTFFYDKRYAETDLSMQPDFVRLAESFGGVGYRVKTKDEFDKALDDAIS-KGVVALIDV 537

Query: 558 QTDPTENVWPMVQAGKGISEMLLGAED 584
             D  ENV PMV AG  +  MLL  +D
Sbjct: 538 VIDRYENVLPMVPAGGSLYNMLLEYKD 564


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: 885
Number of extensions: 38
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: 564
Length adjustment: 36
Effective length of query: 549
Effective length of database: 528
Effective search space:   289872
Effective search space used:   289872
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_084275805.1 B8779_RS06920 (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.9788.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.4e-249  813.0   0.3   7.4e-249  812.7   0.3    1.0  1  lcl|NCBI__GCF_900176045.1:WP_084275805.1  B8779_RS06920 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900176045.1:WP_084275805.1  B8779_RS06920 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  812.7   0.3  7.4e-249  7.4e-249       1     555 [.       4     560 ..       4     562 .. 0.99

  Alignments for each domain:
  == domain 1  score: 812.7 bits;  conditional E-value: 7.4e-249
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               ++ga+++ve++++egve+vfGyPGGa++++yd++y +  +ehil+rheqaa+haadGyara+GkvGv++
  lcl|NCBI__GCF_900176045.1:WP_084275805.1   4 MSGAQMVVEAMREEGVEVVFGYPGGAIMNVYDEIYkHRYFEHILTRHEQAAVHAADGYARATGKVGVAF 72 
                                               79*********************************7788****************************** PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPG tn+vtg+atay+ds+Plvv++Gqv+ s+iG+dafqeid +Gi++p+tkh++lvk+ae+lp+i
  lcl|NCBI__GCF_900176045.1:WP_084275805.1  73 VTSGPGFTNAVTGLATAYMDSIPLVVVSGQVPLSMIGTDAFQEIDAVGISRPCTKHNYLVKSAEELPHI 141
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206
                                               l eaf+ia +GrPGPv+vd+Pkdvt++  e++++++++l +ykpt+kg+ +qikka+e+i++akkPv +
  lcl|NCBI__GCF_900176045.1:WP_084275805.1 142 LAEAFYIARSGRPGPVHVDIPKDVTAQIAEFNYPKEIKLETYKPTIKGNARQIKKAIEAIAQAKKPVFY 210
                                               ********************************************************************* PP

                                 TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275
                                                GgG+i++++ + ++el+++++ip + tl+  G++  d++l lgm+GmhGt++an+a+seadllia+G 
  lcl|NCBI__GCF_900176045.1:WP_084275805.1 211 LGGGIIHSNSADLVRELVQATQIPAVETLMARGTLRYDDELLLGMVGMHGTYAANMAMSEADLLIALGP 279
                                               ********************************************************************* PP

                                 TIGR00118 276 rfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee.ekkeke.Wlek 342
                                               rfddrvtg+l++fa+ a+iih+didP++igk v+vd pivGd kkvlee++ ++ke+ + +  e W + 
  lcl|NCBI__GCF_900176045.1:WP_084275805.1 280 RFDDRVTGKLSEFAKYAQIIHVDIDPSSIGKLVHVDYPIVGDLKKVLEEMVPQAKEKvDPSRYEpWRDI 348
                                               ***************************************************99998876666667**** PP

                                 TIGR00118 343 ieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGt 411
                                               ++++ + ++l+++ ++e +kP  vi+++ + lk++a ++tdvGqhqmw+aqfy++++pr+fitsgGlGt
  lcl|NCBI__GCF_900176045.1:WP_084275805.1 349 LRRYNELHPLTYEDSDEVLKPEWVIQRVGEKLKGKARISTDVGQHQMWTAQFYPFTRPREFITSGGLGT 417
                                               ********************************************************************* PP

                                 TIGR00118 412 mGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyee 480
                                               mGfG+Paa+G+k + p+e  v+++Gdgs+ mn+qel t+vey +pv+ +ilnn++lGmv+qWq +fy++
  lcl|NCBI__GCF_900176045.1:WP_084275805.1 418 MGFGFPAAMGVKKGIPDEISVNISGDGSILMNIQELMTAVEYRLPVINIILNNNYLGMVRQWQTFFYDK 486
                                               ********************************************************************* PP

                                 TIGR00118 481 rysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGag 549
                                               ry+et l+  +pdfv+lae++G +g r+++++e +++l++a+++   +l+dv++d+ e+vlPmv+ G++
  lcl|NCBI__GCF_900176045.1:WP_084275805.1 487 RYAETDLSM-QPDFVRLAESFGGVGYRVKTKDEFDKALDDAISKGVVALIDVVIDRYENVLPMVPAGGS 554
                                               ********6.*********************************************************** PP

                                 TIGR00118 550 ldelve 555
                                               l +++ 
  lcl|NCBI__GCF_900176045.1:WP_084275805.1 555 LYNMLL 560
                                               *99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (564 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: 00:00:00.04
# Mc/sec: 7.80
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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