Alignments for a candidate for ilvI in Desulfacinum infernum DSM 9756

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Desulfacinum infernum DSM 9756

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_073040956.1 BUB04_RS15035 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_900129305.1:WP_073040956.1
          Length = 572

 Score =  634 bits (1635), Expect = 0.0
 Identities = 323/573 (56%), Positives = 406/573 (70%), Gaps = 13/573 (2%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           ++ GA+I    L  E VE ++G+PGGAV+ IY E+ K     HILVRHEQ A H ADGYA
Sbjct: 2   KLTGAQIFFECLKRENVEVIFGFPGGAVIDIYHEMPKHD-IRHILVRHEQGAAHMADGYA 60

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           RATGKVGV LVTSGPG TN VTGIATAY+DS+PMVV TG VPT  IG DAFQE D VGIT
Sbjct: 61  RATGKVGVCLVTSGPGATNTVTGIATAYMDSVPMVVFTGQVPTALIGNDAFQEVDIVGIT 120

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP  KHN+LVKDVRDLA  I++AF++A+TGRPGPV+VD+PKDV + + ++ YP+ + +  
Sbjct: 121 RPCTKHNYLVKDVRDLARVIREAFYLASTGRPGPVLVDLPKDVIQASTEFRYPRKVQLPG 180

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           Y P  + H+GQI +A  LL+ A+RP IY GGGV++++A  EL QLA     PVT TLMGL
Sbjct: 181 YRPTVEPHTGQINRAWELLKKAKRPVIYAGGGVIISSAHQELTQLAEALQAPVTTTLMGL 240

Query: 258 GAFPGTSKQ----------FVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHF 307
           G FP   +           ++GMLGMHGT+ ANMA+QNCDVL A+GARFDDRV G    F
Sbjct: 241 GGFPAVVRNAKGEREMHPLWLGMLGMHGTFRANMAVQNCDVLFAVGARFDDRVTGKIDGF 300

Query: 308 TSQARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQ 367
             +A KI+HID+DP+SISK V VDIPIVG+ K  L++L    K   I+   E  A W +Q
Sbjct: 301 APKA-KIVHIDVDPTSISKNVLVDIPIVGDCKAALRKLNEIAKKDPIENVTETRAPWLDQ 359

Query: 368 IEQWRSVDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRR 427
           I QWR    L Y +    IKPQYVVEKI+EL   +A I ++VGQ+QMW AQ+Y F +PR 
Sbjct: 360 IRQWRETYPLAYKKEGNGIKPQYVVEKIFELADENAIITTEVGQNQMWTAQYYHFAKPRT 419

Query: 428 WINSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSL 487
            + SGGLGTMG GLP A+G + AFP++ V+ + G+GSIQM IQE+ T + +D PVK+  L
Sbjct: 420 LLTSGGLGTMGYGLPAAIGAQAAFPDRLVIDVAGDGSIQMNIQEMITAVCHDLPVKVAIL 479

Query: 488 NNGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFR 547
           NN +LGMVRQWQE+ Y+  Y  + +DA PDFV+LAEAYG VG+R +   +VEP LREA  
Sbjct: 480 NNRFLGMVRQWQELFYEKNYCATCLDASPDFVRLAEAYGAVGLRAKTMEEVEPVLREALS 539

Query: 548 LKDRTVFLDFQTDPTENVWPMVQAGKGISEMLL 580
           ++ + V +DF   P E V+PMV AGK ISEMLL
Sbjct: 540 IR-KPVLMDFWVSPEEGVYPMVPAGKNISEMLL 571


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: 931
Number of extensions: 31
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: 572
Length adjustment: 36
Effective length of query: 549
Effective length of database: 536
Effective search space:   294264
Effective search space used:   294264
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_073040956.1 BUB04_RS15035 (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.24471.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.1e-264  862.0   0.1   1.1e-263  861.8   0.1    1.0  1  lcl|NCBI__GCF_900129305.1:WP_073040956.1  BUB04_RS15035 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900129305.1:WP_073040956.1  BUB04_RS15035 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  861.8   0.1  1.1e-263  1.1e-263       1     554 [.       3     570 ..       3     572 .] 0.97

  Alignments for each domain:
  == domain 1  score: 861.8 bits;  conditional E-value: 1.1e-263
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               l+ga+i+ e lk+e+ve++fG+PGGav++iy ++ + +++hilvrheq+aah+adGyara+GkvGv+l+
  lcl|NCBI__GCF_900129305.1:WP_073040956.1   3 LTGAQIFFECLKRENVEVIFGFPGGAVIDIYHEMPKHDIRHILVRHEQGAAHMADGYARATGKVGVCLV 71 
                                               68******************************************************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatn+vtgiatay+dsvP+vv+tGqv+t+liG+dafqe+di+Git+p+tkh++lvk+++dl++++
  lcl|NCBI__GCF_900129305.1:WP_073040956.1  72 TSGPGATNTVTGIATAYMDSVPMVVFTGQVPTALIGNDAFQEVDIVGITRPCTKHNYLVKDVRDLARVI 140
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               +eaf++astGrPGPvlvdlPkdv +a++e+++++kv+lpgy+ptv++h+ qi++a el++kak+Pv+++
  lcl|NCBI__GCF_900129305.1:WP_073040956.1 141 REAFYLASTGRPGPVLVDLPKDVIQASTEFRYPRKVQLPGYRPTVEPHTGQINRAWELLKKAKRPVIYA 209
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafp..........edhplalgmlGmhGtkeanlavse 266
                                               GgGvii+ a++el++lae+l++pvtttl+GlG+fp          e hpl lgmlGmhGt  an+av++
  lcl|NCBI__GCF_900129305.1:WP_073040956.1 210 GGGVIISSAHQELTQLAEALQAPVTTTLMGLGGFPavvrnakgerEMHPLWLGMLGMHGTFRANMAVQN 278
                                               **********************************955544444444699******************** PP

                                 TIGR00118 267 adlliavGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee... 332
                                               +d+l+avGarfddrvtg+++ fap+aki+hid+dP++i+knv vdipivGd+k  l++l + +k+    
  lcl|NCBI__GCF_900129305.1:WP_073040956.1 279 CDVLFAVGARFDDRVTGKIDGFAPKAKIVHIDVDPTSISKNVLVDIPIVGDCKAALRKLNEIAKKDpie 347
                                               ***********************************************************9988887776 PP

                                 TIGR00118 333 ekkeke..WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkk 399
                                               + +e++  Wl++i++w+++y+l++++e + ikPq+v++++ +l++++ai+tt+vGq+qmw+aq+y++ k
  lcl|NCBI__GCF_900129305.1:WP_073040956.1 348 NVTETRapWLDQIRQWRETYPLAYKKEGNGIKPQYVVEKIFELADENAIITTEVGQNQMWTAQYYHFAK 416
                                               44555557************************************************************* PP

                                 TIGR00118 400 prkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellG 468
                                               pr+ +tsgGlGtmG+GlPaa+Ga+ a p+  v++v+Gdgs+qmn+qe+ t+v  d+pvk+ ilnn++lG
  lcl|NCBI__GCF_900129305.1:WP_073040956.1 417 PRTLLTSGGLGTMGYGLPAAIGAQAAFPDRLVIDVAGDGSIQMNIQEMITAVCHDLPVKVAILNNRFLG 485
                                               ********************************************************************* PP

                                 TIGR00118 469 mvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdke 537
                                               mv+qWqelfye+ y +t+l + +pdfv+laeayG++g+r ++ ee+e  l+eal+ ++pvl+d+ v  e
  lcl|NCBI__GCF_900129305.1:WP_073040956.1 486 MVRQWQELFYEKNYCATCLDA-SPDFVRLAEAYGAVGLRAKTMEEVEPVLREALSIRKPVLMDFWVSPE 553
                                               ********************5.*********************************************** PP

                                 TIGR00118 538 eevlPmvapGagldelv 554
                                               e v+Pmv+ G++++e++
  lcl|NCBI__GCF_900129305.1:WP_073040956.1 554 EGVYPMVPAGKNISEML 570
                                               ***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (572 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: 7.92
//
[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