Alignments for a candidate for ilvI in Desulfotomaculum ruminis DSM 2154

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Desulfotomaculum ruminis DSM 2154

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_013840432.1 DESRU_RS01875 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000215085.1:WP_013840432.1
          Length = 553

 Score =  562 bits (1449), Expect = e-164
 Identities = 289/560 (51%), Positives = 368/560 (65%), Gaps = 10/560 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           E+  AE LV  L  EGVE V+GYPGGA+L +YD L+  +K +HIL RHEQ A HAA GYA
Sbjct: 2   EITCAEALVRCLELEGVELVFGYPGGAILPVYDALN-DSKIKHILTRHEQGAAHAASGYA 60

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R TGKVGV + TSGPG TN VTG+A AY+DSIP+V ITG VPT  +G DAFQE D  GIT
Sbjct: 61  RTTGKVGVCMATSGPGATNLVTGLANAYMDSIPLVAITGQVPTSQVGTDAFQEVDITGIT 120

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
            PI KHN+LVKD + L   +++AF IA TGRPGPV++D+PKDV+    K+ YP+ + ++ 
Sbjct: 121 IPITKHNYLVKDAKTLPLIVRRAFHIARTGRPGPVLIDLPKDVANTRIKFNYPEEVHLKG 180

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           Y P  KGH  QI +A  L+  AERP IY GGGVV A AS+EL  LA     PV  TLMGL
Sbjct: 181 YKPTVKGHIAQINQAAKLMMQAERPVIYAGGGVVNAEASEELVWLAETLDAPVVTTLMGL 240

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           GAFPG  + F+GM G+HG   AN+A+ + D+LI +GARFDDRV G  A F   AR +IH+
Sbjct: 241 GAFPGDHRLFLGMPGLHGNLAANLAVTHSDLLITLGARFDDRVTGRIAGFAPGAR-VIHV 299

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCL 377
           DIDP+ ISK V   +PIVG+ K VL +L+ ++        ++    W EQ+  W+     
Sbjct: 300 DIDPAEISKNVISHLPIVGDTKKVLTDLLVRL-------DKKQNPGWIEQVSSWKEEHAH 352

Query: 378 KYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437
           +Y +  E++KPQYV+E+I+  +KGD  + +DVGQHQMW AQ + F EPR  + SGGLG M
Sbjct: 353 RYQQEGELLKPQYVIEEIYRHSKGDVIVSTDVGQHQMWVAQHFPFKEPRALVTSGGLGVM 412

Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497
           G GLP A+G +   PEK VV +TG+GS QM + ELST  + + P+KI  LNN  LGMVRQ
Sbjct: 413 GFGLPGAIGAQIGRPEKTVVLVTGDGSFQMSLNELSTAAEQELPLKIVVLNNRCLGMVRQ 472

Query: 498 WQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDF 557
            QE   + RY+      +PDF  LA  YG  G  V    +++ AL EAF+     V +D 
Sbjct: 473 LQEFYCEKRYTAVDFGFVPDFAALARVYGFKGYTVNTAEELQSALTEAFQ-DPGPVLIDC 531

Query: 558 QTDPTENVWPMVQAGKGISE 577
             DP ENV PMV AGK I +
Sbjct: 532 SVDPNENVLPMVLAGKDICD 551


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: 909
Number of extensions: 35
Number of successful extensions: 6
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: 553
Length adjustment: 36
Effective length of query: 549
Effective length of database: 517
Effective search space:   283833
Effective search space used:   283833
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_013840432.1 DESRU_RS01875 (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.16614.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.2e-251  820.1   0.0   5.2e-251  819.8   0.0    1.0  1  lcl|NCBI__GCF_000215085.1:WP_013840432.1  DESRU_RS01875 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000215085.1:WP_013840432.1  DESRU_RS01875 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  819.8   0.0  5.2e-251  5.2e-251       2     549 ..       4     548 ..       3     552 .. 0.99

  Alignments for each domain:
  == domain 1  score: 819.8 bits;  conditional E-value: 5.2e-251
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlat 70 
                                               + ae+lv+ l+ egve vfGyPGGa+lp+ydal ds+++hil+rheq+aahaa Gyar++GkvGv++at
  lcl|NCBI__GCF_000215085.1:WP_013840432.1   4 TCAEALVRCLELEGVELVFGYPGGAILPVYDALNDSKIKHILTRHEQGAAHAASGYARTTGKVGVCMAT 72 
                                               679****************************************************************** PP

                                 TIGR00118  71 sGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilk 139
                                               sGPGatnlvtg+a+ay+ds+Plv++tGqv+ts +G+dafqe+di+Git+p+tkh++lvk+a+ lp i++
  lcl|NCBI__GCF_000215085.1:WP_013840432.1  73 SGPGATNLVTGLANAYMDSIPLVAITGQVPTSQVGTDAFQEVDITGITIPITKHNYLVKDAKTLPLIVR 141
                                               ********************************************************************* PP

                                 TIGR00118 140 eafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvG 208
                                               +af+ia tGrPGPvl+dlPkdv+++ i+++++e+v+l+gykptvkgh +qi++a++l+++a++Pv+++G
  lcl|NCBI__GCF_000215085.1:WP_013840432.1 142 RAFHIARTGRPGPVLIDLPKDVANTRIKFNYPEEVHLKGYKPTVKGHIAQINQAAKLMMQAERPVIYAG 210
                                               ********************************************************************* PP

                                 TIGR00118 209 gGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarf 277
                                               gGv+ aeaseel+ lae+l++pv+ttl+GlGafp dh+l+lgm G+hG  +anlav+++dlli++Garf
  lcl|NCBI__GCF_000215085.1:WP_013840432.1 211 GGVVNAEASEELVWLAETLDAPVVTTLMGLGAFPGDHRLFLGMPGLHGNLAANLAVTHSDLLITLGARF 279
                                               ********************************************************************* PP

                                 TIGR00118 278 ddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieew 346
                                               ddrvtg +a fap a++ih+didPaei+knv +++pivGd+kkvl++ll +l ++++    W+e++++w
  lcl|NCBI__GCF_000215085.1:WP_013840432.1 280 DDRVTGRIAGFAPGARVIHVDIDPAEISKNVISHLPIVGDTKKVLTDLLVRLDKKQNPG--WIEQVSSW 346
                                               ****************************************************9988877..******** PP

                                 TIGR00118 347 kkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfG 415
                                               k+e+  ++++e e +kPq+vi+e+++  k+++iv+tdvGqhqmw+aq++++k+pr  +tsgGlG mGfG
  lcl|NCBI__GCF_000215085.1:WP_013840432.1 347 KEEHAHRYQQEGELLKPQYVIEEIYRHSKGDVIVSTDVGQHQMWVAQHFPFKEPRALVTSGGLGVMGFG 415
                                               ********************************************************************* PP

                                 TIGR00118 416 lPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeeryse 484
                                               lP a+Ga+++ pe+tvv vtGdgsfqm+l+elst++e ++p+kiv+lnn++lGmv+q qe++ e+ry++
  lcl|NCBI__GCF_000215085.1:WP_013840432.1 416 LPGAIGAQIGRPEKTVVLVTGDGSFQMSLNELSTAAEQELPLKIVVLNNRCLGMVRQLQEFYCEKRYTA 484
                                               ********************************************************************* PP

                                 TIGR00118 485 tklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGag 549
                                               + ++  +pdf++la+ yG kg ++++ eel+++l+ea++  +pvl+d +vd +e+vlPmv  G+ 
  lcl|NCBI__GCF_000215085.1:WP_013840432.1 485 VDFGF-VPDFAALARVYGFKGYTVNTAEELQSALTEAFQDPGPVLIDCSVDPNENVLPMVLAGKD 548
                                               ****6.*******************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (553 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: 12.17
//
[ok]

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

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Steps (tab-delimited)
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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