Alignments for a candidate for ilvI in Desulfallas geothermicus DSM 3669

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Desulfallas geothermicus DSM 3669

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_092483009.1 BM299_RS08300 biosynthetic-type acetolactate synthase large subunit

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



>NCBI__GCF_900115975.1:WP_092483009.1
          Length = 555

 Score =  581 bits (1497), Expect = e-170
 Identities = 296/563 (52%), Positives = 383/563 (68%), Gaps = 12/563 (2%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           EM  AE LV  L +E +E ++GYPGGA L ++D LH  +   HILVRHEQ AVHAADGYA
Sbjct: 2   EMTAAEALVKCLEKEQLEVIFGYPGGATLPVHDALH-HSSIRHILVRHEQGAVHAADGYA 60

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           RATG+VGV L TSGPG TN +TGIA AY+DS+P+V+ TG VPT  +G DAFQE D  GIT
Sbjct: 61  RATGRVGVCLATSGPGATNLITGIANAYMDSVPLVLFTGQVPTSQVGTDAFQEVDITGIT 120

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
            PI KHN+LVKD   L   IK AF IA+TGRPGPV++D+PKDV++   ++ YP+++ +R 
Sbjct: 121 MPITKHNYLVKDAAQLPRIIKNAFHIASTGRPGPVLIDLPKDVAQTMIEFNYPETVQLRG 180

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           Y P  +GH+G+I +A  L+  + RP IY GGG++ + AS EL  LA     PVTNT MGL
Sbjct: 181 YKPTYRGHAGKIAEAARLIARSSRPVIYAGGGIINSRASKELLALAETINAPVTNTFMGL 240

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
            +FPG    F+GMLG+HGT  AN+A+ NCD+LIA+GARFDDRV G  A F  +A  +IH+
Sbjct: 241 SSFPGDHPLFLGMLGLHGTRTANLAVTNCDLLIALGARFDDRVTGKIAEFAPRA-GVIHV 299

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQI-KASDIKPKREALAKWWEQIEQWRSVDC 376
           DIDP+ I K V+V +PIVG+VK VLQEL+ ++ K SD         +W EQIE W+    
Sbjct: 300 DIDPAEIGKNVQVHVPIVGDVKMVLQELLPRLEKRSD--------TRWLEQIEAWKKEHP 351

Query: 377 LKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGT 436
           L+Y+  +E +KPQYV+EK++E+T+GDA++ +DVGQHQMW AQ+Y+F  P   I+SGGLGT
Sbjct: 352 LRYETGAEELKPQYVIEKLYEITRGDAYVATDVGQHQMWVAQYYRFKRPGGLISSGGLGT 411

Query: 437 MGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVR 496
           MG GLP AMG +   P + VV +TG+GSIQM +QEL T ++ + P+KI  LNN  LGMVR
Sbjct: 412 MGFGLPAAMGAQIGLPGERVVLVTGDGSIQMTMQELGTIMEQELPIKIIILNNHVLGMVR 471

Query: 497 QWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLD 556
           Q Q++  + RY        PDF  LA AY   G  +    DV+  L EA       V ++
Sbjct: 472 QLQKVYCEGRYMAVDFKFHPDFETLARAYRIKGYTLRNKEDVDNLLPEALE-SPGAVLVN 530

Query: 557 FQTDPTENVWPMVQAGKGISEML 579
                 ENV PMV AGK ISE +
Sbjct: 531 CLVSAEENVNPMVLAGKSISEAI 553


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: 906
Number of extensions: 22
Number of successful extensions: 5
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: 555
Length adjustment: 36
Effective length of query: 549
Effective length of database: 519
Effective search space:   284931
Effective search space used:   284931
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_092483009.1 BM299_RS08300 (biosynthetic-type acetolactate synthase large subunit)
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.16888.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-254  831.8   0.0   1.4e-254  831.6   0.0    1.0  1  lcl|NCBI__GCF_900115975.1:WP_092483009.1  BM299_RS08300 biosynthetic-type 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900115975.1:WP_092483009.1  BM299_RS08300 biosynthetic-type acetolactate synthase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  831.6   0.0  1.4e-254  1.4e-254       1     554 [.       3     553 ..       3     555 .] 0.99

  Alignments for each domain:
  == domain 1  score: 831.6 bits;  conditional E-value: 1.4e-254
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               +++ae+lv+ l+ke++e++fGyPGGa lp++dal++s ++hilvrheq+a+haadGyara+G+vGv+la
  lcl|NCBI__GCF_900115975.1:WP_092483009.1   3 MTAAEALVKCLEKEQLEVIFGYPGGATLPVHDALHHSSIRHILVRHEQGAVHAADGYARATGRVGVCLA 71 
                                               789****************************************************************** PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatnl+tgia+ay+dsvPlv++tGqv+ts +G+dafqe+di+Git+p+tkh++lvk+a++lp+i+
  lcl|NCBI__GCF_900115975.1:WP_092483009.1  72 TSGPGATNLITGIANAYMDSVPLVLFTGQVPTSQVGTDAFQEVDITGITMPITKHNYLVKDAAQLPRII 140
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               k+af+iastGrPGPvl+dlPkdv+++ ie++++e+v+l+gykpt +gh  +i++a+ li+++ +Pv+++
  lcl|NCBI__GCF_900115975.1:WP_092483009.1 141 KNAFHIASTGRPGPVLIDLPKDVAQTMIEFNYPETVQLRGYKPTYRGHAGKIAEAARLIARSSRPVIYA 209
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgG+i + as+el  lae++++pvt t++Gl +fp dhpl+lgmlG+hGt++anlav+++dllia+Gar
  lcl|NCBI__GCF_900115975.1:WP_092483009.1 210 GGGIINSRASKELLALAETINAPVTNTFMGLSSFPGDHPLFLGMLGLHGTRTANLAVTNCDLLIALGAR 278
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekiee 345
                                               fddrvtg++a+fap+a +ih+didPaeigknv+v++pivGd+k vl+ell +l++++  +++Wle+ie 
  lcl|NCBI__GCF_900115975.1:WP_092483009.1 279 FDDRVTGKIAEFAPRAGVIHVDIDPAEIGKNVQVHVPIVGDVKMVLQELLPRLEKRS--DTRWLEQIEA 345
                                               ****************************************************98765..556******* PP

                                 TIGR00118 346 wkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGf 414
                                               wkke++l++++  e++kPq+vi++l+++++++a+v+tdvGqhqmw+aq+y++k+p   i+sgGlGtmGf
  lcl|NCBI__GCF_900115975.1:WP_092483009.1 346 WKKEHPLRYETGAEELKPQYVIEKLYEITRGDAYVATDVGQHQMWVAQYYRFKRPGGLISSGGLGTMGF 414
                                               ********************************************************************* PP

                                 TIGR00118 415 GlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerys 483
                                               GlPaa+Ga+++ p e vv vtGdgs+qm++qel ti+e ++p+ki+ilnn++lGmv+q q+++ e+ry 
  lcl|NCBI__GCF_900115975.1:WP_092483009.1 415 GLPAAMGAQIGLPGERVVLVTGDGSIQMTMQELGTIMEQELPIKIIILNNHVLGMVRQLQKVYCEGRYM 483
                                               ********************************************************************* PP

                                 TIGR00118 484 etklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGaglde 552
                                               ++ ++  +pdf+ la+ay +kg +++++e++++ l eales + vl++  v  ee+v Pmv  G++++e
  lcl|NCBI__GCF_900115975.1:WP_092483009.1 484 AVDFKF-HPDFETLARAYRIKGYTLRNKEDVDNLLPEALESPGAVLVNCLVSAEENVNPMVLAGKSISE 551
                                               *****6.***********************************************************999 PP

                                 TIGR00118 553 lv 554
                                                +
  lcl|NCBI__GCF_900115975.1:WP_092483009.1 552 AI 553
                                               77 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (555 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 12.50
//
[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