Alignments for a candidate for ilvI in Denitrovibrio acetiphilus DSM 12809

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Denitrovibrio acetiphilus DSM 12809

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_013009758.1 DACET_RS02085 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000025725.1:WP_013009758.1
          Length = 563

 Score =  624 bits (1610), Expect = 0.0
 Identities = 295/563 (52%), Positives = 406/563 (72%), Gaps = 2/563 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           +M GAEILV +L ++GV+ ++GYPGG +L IYD L   +  +HIL RHEQ  +HAADGYA
Sbjct: 2   KMTGAEILVESLRKQGVDLIFGYPGGVLLGIYDTLF-DSDIKHILPRHEQGGIHAADGYA 60

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           RATGKVGV   TSGPG TN VTGI  A++DS+P+VV TG V ++ IG DAFQE D +GIT
Sbjct: 61  RATGKVGVCFGTSGPGATNLVTGICNAHMDSVPLVVFTGQVASNLIGGDAFQEADIIGIT 120

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RPIVKH++L+ +  ++   I++AF+IAA+GRPGPVV+D+PKD+     ++++P  I++  
Sbjct: 121 RPIVKHSYLINNPEEITTVIREAFYIAASGRPGPVVIDLPKDIMAQKAEFKWPSKIELPG 180

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           YNP  KGH GQI+K + +L+GA++P IY GGGV+L+ AS+E+ +L+ LTG PV ++ +G 
Sbjct: 181 YNPTVKGHLGQIKKMLRMLEGAKKPVIYMGGGVILSGASEEMTKLSELTGVPVISSFLGQ 240

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           G  PGT + ++G LGMHG Y +NMAM   D ++A+G RF DR  G    F   A K+ HI
Sbjct: 241 GGIPGTHENYIGWLGMHGNYASNMAMAEPDFILAVGTRFSDRSTGRLDGFAPNA-KVAHI 299

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCL 377
           D+DPSSISK V++D+PIVG+ K VL + +++I         +A   W E+I+ W      
Sbjct: 300 DVDPSSISKNVRIDVPIVGDCKVVLNQALSEIDKYSWDKNLKARKDWMEKIKAWDKKQPF 359

Query: 378 KYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437
            YDR S +IKPQYVVE I+++TKG+A IC++VGQ+QMWA QFYK+  PR++++SGGLGTM
Sbjct: 360 GYDRESTLIKPQYVVESIYKVTKGEAIICTEVGQNQMWAGQFYKYKNPRQFVSSGGLGTM 419

Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497
           G G P A+G K   P+KEV  I G+GS  M IQE+ T +QY+  VK+  LNN YLGM+RQ
Sbjct: 420 GYGFPAAIGAKLGCPDKEVFDIAGDGSFMMNIQEICTAVQYNVAVKVAILNNKYLGMIRQ 479

Query: 498 WQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDF 557
           WQ + ++NRYS   +D  PDFVKLAE++  VGMR+++  DVE A+RE+ ++KD+ V +DF
Sbjct: 480 WQNMFFNNRYSQCCLDCQPDFVKLAESFNAVGMRIDRKEDVEGAIRESLKIKDKPVIMDF 539

Query: 558 QTDPTENVWPMVQAGKGISEMLL 580
             D  ENV+PM+ AG  I+EMLL
Sbjct: 540 TVDREENVFPMIPAGAAINEMLL 562


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: 902
Number of extensions: 34
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: 585
Length of database: 563
Length adjustment: 36
Effective length of query: 549
Effective length of database: 527
Effective search space:   289323
Effective search space used:   289323
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_013009758.1 DACET_RS02085 (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.20886.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.8e-255  833.2   0.1   5.5e-255  833.0   0.1    1.0  1  lcl|NCBI__GCF_000025725.1:WP_013009758.1  DACET_RS02085 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025725.1:WP_013009758.1  DACET_RS02085 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  833.0   0.1  5.5e-255  5.5e-255       1     554 [.       3     561 ..       3     563 .] 0.98

  Alignments for each domain:
  == domain 1  score: 833.0 bits;  conditional E-value: 5.5e-255
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               ++gaeilvesl+k+gv+ +fGyPGG +l iyd+l+ds+++hil+rheq+ +haadGyara+GkvGv+++
  lcl|NCBI__GCF_000025725.1:WP_013009758.1   3 MTGAEILVESLRKQGVDLIFGYPGGVLLGIYDTLFDSDIKHILPRHEQGGIHAADGYARATGKVGVCFG 71 
                                               79******************************************************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatnlvtgi +a++dsvPlvv+tGqva++liG dafqe+di+Git+p++khs+l++++e++++++
  lcl|NCBI__GCF_000025725.1:WP_013009758.1  72 TSGPGATNLVTGICNAHMDSVPLVVFTGQVASNLIGGDAFQEADIIGITRPIVKHSYLINNPEEITTVI 140
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               +eaf+ia++GrPGPv++dlPkd+++++ e++ ++k+elpgy+ptvkgh  qikk l ++e akkPv+++
  lcl|NCBI__GCF_000025725.1:WP_013009758.1 141 REAFYIAASGRPGPVVIDLPKDIMAQKAEFKWPSKIELPGYNPTVKGHLGQIKKMLRMLEGAKKPVIYM 209
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgGvi ++asee+++l+e + +pv++++lG+G++p +h++ +g lGmhG +++n+a+ e d ++avG+r
  lcl|NCBI__GCF_000025725.1:WP_013009758.1 210 GGGVILSGASEEMTKLSELTGVPVISSFLGQGGIPGTHENYIGWLGMHGNYASNMAMAEPDFILAVGTR 278
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wl 340
                                               f+dr tg l+ fap+ak+ hid+dP++i+knv+ d+pivGd+k vl++ l+++ ++    + k ++ W+
  lcl|NCBI__GCF_000025725.1:WP_013009758.1 279 FSDRSTGRLDGFAPNAKVAHIDVDPSSISKNVRIDVPIVGDCKVVLNQALSEIDKYswdkNLKARKdWM 347
                                               ****************************************************999978763344445** PP

                                 TIGR00118 341 ekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGl 409
                                               eki+ w k++++ +d+e++ ikPq+v+++++k++k+eai+ t+vGq+qmwa qfyk+k+pr+f++sgGl
  lcl|NCBI__GCF_000025725.1:WP_013009758.1 348 EKIKAWDKKQPFGYDRESTLIKPQYVVESIYKVTKGEAIICTEVGQNQMWAGQFYKYKNPRQFVSSGGL 416
                                               ********************************************************************* PP

                                 TIGR00118 410 GtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfy 478
                                               GtmG+G+Paa+Gak++ p+++v +++Gdgsf+mn+qe+ t+v+y++ vk+ ilnn++lGm++qWq++f+
  lcl|NCBI__GCF_000025725.1:WP_013009758.1 417 GTMGYGFPAAIGAKLGCPDKEVFDIAGDGSFMMNIQEICTAVQYNVAVKVAILNNKYLGMIRQWQNMFF 485
                                               ********************************************************************* PP

                                 TIGR00118 479 eerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmvap 546
                                               ++rys+ +l + +pdfvklae++ ++g+ri ++e++e +++e l+ k +pv++d++vd+ee+v+Pm++ 
  lcl|NCBI__GCF_000025725.1:WP_013009758.1 486 NNRYSQCCLDC-QPDFVKLAESFNAVGMRIDRKEDVEGAIRESLKIKdKPVIMDFTVDREENVFPMIPA 553
                                               **********8.********************************98879******************** PP

                                 TIGR00118 547 Gagldelv 554
                                               Ga+++e++
  lcl|NCBI__GCF_000025725.1:WP_013009758.1 554 GAAINEML 561
                                               ******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (563 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: 12.28
//
[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