Alignments for a candidate for ilvI in Sulfurihydrogenibium subterraneum DSM 15120

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Sulfurihydrogenibium subterraneum DSM 15120

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_028951193.1 Q385_RS0108165 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000619805.1:WP_028951193.1
          Length = 581

 Score =  618 bits (1594), Expect = 0.0
 Identities = 310/564 (54%), Positives = 404/564 (71%), Gaps = 7/564 (1%)

Query: 21  GAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYARAT 80
           GA+I+V  L  EGV+ V+G PGGA++ +YD L     F +IL RHEQAA H ADGYARAT
Sbjct: 6   GADIVVDVLIHEGVDTVFGLPGGAIMEVYDALF-DAPFRNILTRHEQAACHMADGYARAT 64

Query: 81  GKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITRPI 140
           GKVGV + TSGPG TN VTG+ATAY+DSIP+V ITG VP H IG DAFQE D +GITRPI
Sbjct: 65  GKVGVVIATSGPGATNLVTGLATAYMDSIPLVAITGQVPRHYIGTDAFQEADVIGITRPI 124

Query: 141 VKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS--- 197
            KHNFLV D++DL   +++AF+IA TGRPGPV+VDIPKD+++   +Y  P   +++    
Sbjct: 125 TKHNFLVTDIKDLPLILRQAFYIARTGRPGPVLVDIPKDITQQVAEYYIPSDEEVKESLP 184

Query: 198 -YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMG 256
            YNP  +G+  QI+KA  L++ A RP +Y GGG +L+ A++E+ +LA LT  PVT T MG
Sbjct: 185 GYNPHVEGNPVQIKKAAELIRKATRPVLYVGGGAILSGAAEEVTKLARLTKIPVTTTNMG 244

Query: 257 LGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIH 316
            GAFP T    + MLGMHGTY ANMA+ + D+LIA+G+RFDDRV G  + F  +A KIIH
Sbjct: 245 KGAFPETDPLSLHMLGMHGTYYANMAVYHSDLLIAVGSRFDDRVTGKISEFAPEA-KIIH 303

Query: 317 IDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDC 376
           IDIDP+SISK + VD+PIVG+VK+VLQ+LI +++   ++    A   W +QI++W+    
Sbjct: 304 IDIDPASISKTITVDVPIVGDVKNVLQKLIKELEEKPVEWVA-ARENWLKQIQEWKEKHP 362

Query: 377 LKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGT 436
           L Y +S +IIKPQYV+E+I+ +T GDA I + VGQHQMWAA FYK+  PR+++NSGGLGT
Sbjct: 363 LSYRKSDKIIKPQYVIEEIYNITNGDAIISAGVGQHQMWAAMFYKYSYPRQFLNSGGLGT 422

Query: 437 MGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVR 496
           MG G P ++G K   PEK V  I G+GS  M IQ+L+T +QY  PVKI  +NNG+LGMVR
Sbjct: 423 MGFGFPASVGAKIGRPEKTVFAIEGDGSFIMNIQDLATAVQYRVPVKIAIINNGFLGMVR 482

Query: 497 QWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLD 556
           QWQ+  YD+RY+   +   PDFVKLAE++G VG+R  K S+V   L +A  + DR V +D
Sbjct: 483 QWQQFFYDSRYASVCLSVQPDFVKLAESFGAVGLRATKPSEVREVLAKAMEINDRPVLID 542

Query: 557 FQTDPTENVWPMVQAGKGISEMLL 580
           F  D  ENV PMV AGK   +M+L
Sbjct: 543 FVVDREENVLPMVPAGKSYRDMIL 566


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: 912
Number of extensions: 37
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: 581
Length adjustment: 36
Effective length of query: 549
Effective length of database: 545
Effective search space:   299205
Effective search space used:   299205
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_028951193.1 Q385_RS0108165 (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.23831.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-262  858.2   0.5   1.5e-262  858.0   0.5    1.0  1  lcl|NCBI__GCF_000619805.1:WP_028951193.1  Q385_RS0108165 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000619805.1:WP_028951193.1  Q385_RS0108165 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  858.0   0.5  1.5e-262  1.5e-262       2     555 ..       5     566 ..       4     568 .. 0.98

  Alignments for each domain:
  == domain 1  score: 858.0 bits;  conditional E-value: 1.5e-262
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlat 70 
                                               +ga+i+v+ l +egv+tvfG PGGa++++ydal+d  ++ il+rheqaa h+adGyara+GkvGvv+at
  lcl|NCBI__GCF_000619805.1:WP_028951193.1   5 RGADIVVDVLIHEGVDTVFGLPGGAIMEVYDALFDAPFRNILTRHEQAACHMADGYARATGKVGVVIAT 73 
                                               79******************************************************************* PP

                                 TIGR00118  71 sGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilk 139
                                               sGPGatnlvtg+atay+ds+Plv++tGqv+++ iG+dafqe+d++Git+p+tkh+flv++ +dlp il+
  lcl|NCBI__GCF_000619805.1:WP_028951193.1  74 SGPGATNLVTGLATAYMDSIPLVAITGQVPRHYIGTDAFQEADVIGITRPITKHNFLVTDIKDLPLILR 142
                                               ********************************************************************* PP

                                 TIGR00118 140 eafeiastGrPGPvlvdlPkdvteaeieleve....ekvelpgykptvkghklqikkaleliekakkPv 204
                                               +af+ia tGrPGPvlvd+Pkd+t++  e+ ++     k +lpgy+p+v+g++ qikka+eli+ka +Pv
  lcl|NCBI__GCF_000619805.1:WP_028951193.1 143 QAFYIARTGRPGPVLVDIPKDITQQVAEYYIPsdeeVKESLPGYNPHVEGNPVQIKKAAELIRKATRPV 211
                                               ************************9999877766444568***************************** PP

                                 TIGR00118 205 llvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273
                                               l+vGgG+i ++a ee+++la  +kipvttt +G+Gafpe++pl+l mlGmhGt++an+av ++dlliav
  lcl|NCBI__GCF_000619805.1:WP_028951193.1 212 LYVGGGAILSGAAEEVTKLARLTKIPVTTTNMGKGAFPETDPLSLHMLGMHGTYYANMAVYHSDLLIAV 280
                                               ********************************************************************* PP

                                 TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke 338
                                               G rfddrvtg++++fapeakiihididPa+i+k+++vd+pivGd+k+vl++l+k+l+e+        ++
  lcl|NCBI__GCF_000619805.1:WP_028951193.1 281 GSRFDDRVTGKISEFAPEAKIIHIDIDPASISKTITVDVPIVGDVKNVLQKLIKELEEKpvewVAAREN 349
                                               *********************************************************998876344446 PP

                                 TIGR00118 339 WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsg 407
                                               Wl++i+ewk++++l++ ++++ ikPq+vi+e++++++++ai++++vGqhqmwaa fyk+++pr+f++sg
  lcl|NCBI__GCF_000619805.1:WP_028951193.1 350 WLKQIQEWKEKHPLSYRKSDKIIKPQYVIEEIYNITNGDAIISAGVGQHQMWAAMFYKYSYPRQFLNSG 418
                                               ********************************************************************* PP

                                 TIGR00118 408 GlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqel 476
                                               GlGtmGfG+Pa++Gak++ pe+tv a+ Gdgsf mn+q+l+t+v+y +pvki i+nn +lGmv+qWq++
  lcl|NCBI__GCF_000619805.1:WP_028951193.1 419 GLGTMGFGFPASVGAKIGRPEKTVFAIEGDGSFIMNIQDLATAVQYRVPVKIAIINNGFLGMVRQWQQF 487
                                               ********************************************************************* PP

                                 TIGR00118 477 fyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmv 544
                                               fy+ ry++++l+  +pdfvklae++G++g+r +kp+e+ e l++a+e + +pvl+d++vd+ee+vlPmv
  lcl|NCBI__GCF_000619805.1:WP_028951193.1 488 FYDSRYASVCLSV-QPDFVKLAESFGAVGLRATKPSEVREVLAKAMEINdRPVLIDFVVDREENVLPMV 555
                                               ************6.*********************************9879****************** PP

                                 TIGR00118 545 apGagldelve 555
                                               + G++  +++ 
  lcl|NCBI__GCF_000619805.1:WP_028951193.1 556 PAGKSYRDMIL 566
                                               ********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (581 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: 7.85
//
[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