Alignments for a candidate for ilvI in Desulfuromonas acetexigens

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Desulfuromonas acetexigens

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_092053014.1 BQ4888_RS02105 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_900111775.1:WP_092053014.1
          Length = 565

 Score =  626 bits (1615), Expect = 0.0
 Identities = 313/564 (55%), Positives = 409/564 (72%), Gaps = 5/564 (0%)

Query: 21  GAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYARAT 80
           G++IL+  L  EGV+ ++GYPGG V+ IYD+L   +  +HIL RHEQAAVHAADGYARA+
Sbjct: 5   GSQILLECLRLEGVDTIFGYPGGTVINIYDDL-MDSPIKHILTRHEQAAVHAADGYARAS 63

Query: 81  GKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITRPI 140
           GKVGVA+ TSGPG TN +TGIATAY+DSIPMV+ITG VPT  IG DAFQE D +GITRPI
Sbjct: 64  GKVGVAIATSGPGATNTITGIATAYMDSIPMVIITGQVPTPLIGNDAFQEADVIGITRPI 123

Query: 141 VKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRSYNP 200
            KHN+LVK+V DLA  IK+AF+IA TGRPGPV+VD+PKDV     ++EYP+++++R Y P
Sbjct: 124 TKHNYLVKNVNDLARIIKQAFYIARTGRPGPVLVDLPKDVQVATAEFEYPETVELRGYKP 183

Query: 201 VNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGLGAF 260
              G+  QI  A  ++  A +P +Y GGGV L+N S EL QLA L   PVT TLM + +F
Sbjct: 184 TYSGNVRQIENAAKMIMAARKPVLYVGGGVTLSNTSQELMQLAELIQAPVTTTLMAMASF 243

Query: 261 PGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHIDID 320
           P      +GMLGMHGTY ANMA+ N D+LI++GARFDDRV G  A F   A KIIHIDID
Sbjct: 244 PKKHPLSLGMLGMHGTYYANMAVTNSDLLISVGARFDDRVTGKIATFAPHA-KIIHIDID 302

Query: 321 PSSISKRVKVDIPIVGNVKDVLQELIAQI--KASDIKPKREALAKWWEQIEQWRSVDCLK 378
           P+SI K V+VD+PIVG++KDVL++L++++  +  +I    EA   W ++I  W++   + 
Sbjct: 303 PTSIKKNVRVDLPIVGDLKDVLKKLVSKLGERKEEIPALVEATEGWRQEINGWKTQHPMS 362

Query: 379 YDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTMG 438
           Y  S  IIKPQ+V+EK+ ELT+ DA I ++VGQHQMW AQF+ F +PR +++SGGLGTMG
Sbjct: 363 YKASKTIIKPQFVIEKLRELTRDDAIITTEVGQHQMWTAQFFDFSQPRTFLSSGGLGTMG 422

Query: 439 VGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQW 498
            GLP A+G + AF E++V+ I+G+GS QM  QEL+T +QY  PVKI  LNN +LGMVRQW
Sbjct: 423 YGLPSALGAQAAFRERQVIDISGDGSFQMNSQELATLVQYRLPVKIVILNNNFLGMVRQW 482

Query: 499 QEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDFQ 558
           Q + + NRYS + M+   DFVKLAEAYG  G+R  K  +VE  +R+A       V ++F+
Sbjct: 483 QHLFFHNRYSQTCMELPIDFVKLAEAYGATGLRATKPEEVEEVIRKALETPG-PVIMEFK 541

Query: 559 TDPTENVWPMVQAGKGISEMLLGA 582
               ENV PMV AG G++EM+L +
Sbjct: 542 ISREENVMPMVPAGAGLNEMVLAS 565


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: 854
Number of extensions: 38
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: 565
Length adjustment: 36
Effective length of query: 549
Effective length of database: 529
Effective search space:   290421
Effective search space used:   290421
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_092053014.1 BQ4888_RS02105 (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.22242.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-265  867.8   1.0   1.8e-265  867.6   1.0    1.0  1  lcl|NCBI__GCF_900111775.1:WP_092053014.1  BQ4888_RS02105 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900111775.1:WP_092053014.1  BQ4888_RS02105 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  867.6   1.0  1.8e-265  1.8e-265       2     555 ..       4     563 ..       3     565 .] 0.98

  Alignments for each domain:
  == domain 1  score: 867.6 bits;  conditional E-value: 1.8e-265
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlat 70 
                                               +g++il+e l+ egv+t+fGyPGG+v++iyd l ds ++hil+rheqaa+haadGyarasGkvGv++at
  lcl|NCBI__GCF_900111775.1:WP_092053014.1   4 TGSQILLECLRLEGVDTIFGYPGGTVINIYDDLMDSPIKHILTRHEQAAVHAADGYARASGKVGVAIAT 72 
                                               799****************************************************************** PP

                                 TIGR00118  71 sGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilk 139
                                               sGPGatn++tgiatay+ds+P+v++tGqv+t liG+dafqe+d++Git+p+tkh++lvk+++dl++i+k
  lcl|NCBI__GCF_900111775.1:WP_092053014.1  73 SGPGATNTITGIATAYMDSIPMVIITGQVPTPLIGNDAFQEADVIGITRPITKHNYLVKNVNDLARIIK 141
                                               ********************************************************************* PP

                                 TIGR00118 140 eafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvG 208
                                               +af+ia tGrPGPvlvdlPkdv+ a+ e+e++e+vel+gykpt +g+ +qi++a+++i++a+kPvl+vG
  lcl|NCBI__GCF_900111775.1:WP_092053014.1 142 QAFYIARTGRPGPVLVDLPKDVQVATAEFEYPETVELRGYKPTYSGNVRQIENAAKMIMAARKPVLYVG 210
                                               ********************************************************************* PP

                                 TIGR00118 209 gGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarf 277
                                               gGv  +++s+el++lae +++pvtttl+ + +fp++hpl+lgmlGmhGt++an+av+++dlli+vGarf
  lcl|NCBI__GCF_900111775.1:WP_092053014.1 211 GGVTLSNTSQELMQLAELIQAPVTTTLMAMASFPKKHPLSLGMLGMHGTYYANMAVTNSDLLISVGARF 279
                                               ********************************************************************* PP

                                 TIGR00118 278 ddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee.......ekkeke. 338
                                               ddrvtg++a+fap+akiihididP++i knv+vd+pivGd k vl++l++kl e+        +  +e 
  lcl|NCBI__GCF_900111775.1:WP_092053014.1 280 DDRVTGKIATFAPHAKIIHIDIDPTSIKKNVRVDLPIVGDLKDVLKKLVSKLGERkeeipalVE-ATEg 347
                                               ***************************************************9887666776423.3345 PP

                                 TIGR00118 339 WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsg 407
                                               W ++i+ wk++++++++ +++ ikPq vi++l +l++d+ai+tt+vGqhqmw+aqf+++++pr+f++sg
  lcl|NCBI__GCF_900111775.1:WP_092053014.1 348 WRQEINGWKTQHPMSYKASKTIIKPQFVIEKLRELTRDDAIITTEVGQHQMWTAQFFDFSQPRTFLSSG 416
                                               ********************************************************************* PP

                                 TIGR00118 408 GlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqel 476
                                               GlGtmG+GlP+alGa+ a  e +v++++Gdgsfqmn qel+t+v+y +pvkivilnn++lGmv+qWq+l
  lcl|NCBI__GCF_900111775.1:WP_092053014.1 417 GLGTMGYGLPSALGAQAAFRERQVIDISGDGSFQMNSQELATLVQYRLPVKIVILNNNFLGMVRQWQHL 485
                                               ********************************************************************* PP

                                 TIGR00118 477 fyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmva 545
                                               f+++rys+t+++    dfvklaeayG++g+r +kpee+ee +++ale+ +pv++++++ +ee+v+Pmv+
  lcl|NCBI__GCF_900111775.1:WP_092053014.1 486 FFHNRYSQTCMEL-PIDFVKLAEAYGATGLRATKPEEVEEVIRKALETPGPVIMEFKISREENVMPMVP 553
                                               ************6.88***************************************************** PP

                                 TIGR00118 546 pGagldelve 555
                                                Gagl+e+v 
  lcl|NCBI__GCF_900111775.1:WP_092053014.1 554 AGAGLNEMVL 563
                                               ********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (565 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: 00:00:00.03
# Mc/sec: 7.88
//
[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