Alignments for a candidate for ilvI in Bacillus alkalinitrilicus DSM 22532

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Bacillus alkalinitrilicus DSM 22532

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_078430191.1 BK574_RS22730 acetolactate synthase, large subunit, biosynthetic type

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_002019605.1:WP_078430191.1
          Length = 574

 Score =  558 bits (1437), Expect = e-163
 Identities = 293/574 (51%), Positives = 388/574 (67%), Gaps = 17/574 (2%)

Query: 36  QQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASGY 95
           Q L+G+  +IR+L + GVDVIFG PGGA+LP YD ++ S  +RH+L RHEQGA HAA GY
Sbjct: 17  QPLSGSSMLIRALAKEGVDVIFGYPGGAILPTYDEIYKSG-IRHILARHEQGAIHAAEGY 75

Query: 96  AHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGI 155
           A V+G+ GVC+ TSGPGATN+VT +ADA +DS+P+V ITGQV   +IGTDAFQEAD+ GI
Sbjct: 76  ARVSGKPGVCIVTSGPGATNVVTGIADAMIDSLPLVVITGQVATSVIGTDAFQEADMIGI 135

Query: 156 TMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRMELP 215
           TMPITKHNF VR  +++PR++ EAFHIA +GRPG VL+D+PKDV      F++   ++LP
Sbjct: 136 TMPITKHNFQVRKVEELPRIMKEAFHIATTGRPGPVLIDLPKDVSVATGLFNYDKEVDLP 195

Query: 216 GYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLMA 275
           GY+P   P+  Q+R+ A+ +A A+KP +  G GV+   A ++L E AE   IPV +TL+ 
Sbjct: 196 GYQPTVIPNKLQIRKLAEAVAEAKKPCILSGAGVLHAHAYDELFEYAEKMRIPVASTLLG 255

Query: 276 RGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKVIHA 335
            GAFP  +   LGM GMHGT AA  A+ +SDLLI++G RFDDR+TG L  FAP AK+ H 
Sbjct: 256 LGAFPGENELFLGMAGMHGTYAANMAIHQSDLLISIGARFDDRLTGALQHFAPNAKIAHI 315

Query: 336 DIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADWWAYLNGVRKTYPLS 395
           DIDPAEIGKN    +P+VGD KA +  L   L  +   G  E   W A L  ++  YPL 
Sbjct: 316 DIDPAEIGKNIETAIPVVGDAKAALKML---LEENGAVG--ETGVWLAELTKMKAEYPLW 370

Query: 396 YGPQSDG-SLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGLGT 454
           Y  + DG ++ P+ ++E + E+   +A+    VGQHQMWAAQ+ ++ KP  W+ SGGLGT
Sbjct: 371 Y--KEDGETIKPQKLMELIYEVTNGEAIVTTDVGQHQMWAAQYYKFNKPNRWVTSGGLGT 428

Query: 455 MGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGMVR 514
           MGF  PAA+GA+ A P T V +I GD  FQMT QEL+      +PVK+ ++NN  LGMVR
Sbjct: 429 MGFGFPAAIGAQFAEPDTPVVSILGDAGFQMTAQELSILQDLNLPVKIIIVNNSALGMVR 488

Query: 515 QWQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQARAINDCP 574
           QWQ LFY ERYS +   T     P+FVKLAEA    G+R ++ EDV   + +A A +D P
Sbjct: 489 QWQQLFYEERYSNSVFNTQ----PNFVKLAEAYDVKGMRIDKVEDVKGALEEALA-HDGP 543

Query: 575 VVIDFIVGADAQVWPMVAAGTSNDEIQAARGIRP 608
           V++DF V     V+PM+A G    E++   GI+P
Sbjct: 544 VLMDFRVTQVENVYPMIAPGKGQHEME---GIKP 574


Lambda     K      H
   0.319    0.136    0.414 

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: 1045
Number of extensions: 45
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: 618
Length of database: 574
Length adjustment: 37
Effective length of query: 581
Effective length of database: 537
Effective search space:   311997
Effective search space used:   311997
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_078430191.1 BK574_RS22730 (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.32684.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.2e-267  872.7   2.0   5.9e-267  872.5   2.0    1.0  1  lcl|NCBI__GCF_002019605.1:WP_078430191.1  BK574_RS22730 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002019605.1:WP_078430191.1  BK574_RS22730 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  872.5   2.0  5.9e-267  5.9e-267       1     554 [.      19     570 ..      19     573 .. 0.99

  Alignments for each domain:
  == domain 1  score: 872.5 bits;  conditional E-value: 5.9e-267
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               l+g+++l+++l kegv+++fGyPGGa+lp yd++y+s+++hil+rheq+a+haa+Gyar+sGk+Gv+++
  lcl|NCBI__GCF_002019605.1:WP_078430191.1  19 LSGSSMLIRALAKEGVDVIFGYPGGAILPTYDEIYKSGIRHILARHEQGAIHAAEGYARVSGKPGVCIV 87 
                                               5899***************************************************************** PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatn+vtgia+a++ds+Plvv+tGqvats+iG+dafqe+d++Git+p+tkh+f+v+k+e+lp+i+
  lcl|NCBI__GCF_002019605.1:WP_078430191.1  88 TSGPGATNVVTGIADAMIDSLPLVVITGQVATSVIGTDAFQEADMIGITMPITKHNFQVRKVEELPRIM 156
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               keaf+ia+tGrPGPvl+dlPkdv+ a+  ++++++v+lpgy+ptv ++klqi+k++e++++akkP +l 
  lcl|NCBI__GCF_002019605.1:WP_078430191.1 157 KEAFHIATTGRPGPVLIDLPKDVSVATGLFNYDKEVDLPGYQPTVIPNKLQIRKLAEAVAEAKKPCILS 225
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               G+Gv++a+a +el e+ae+++ipv++tllGlGafp +++l+lgm+GmhGt++an+a++++dlli++Gar
  lcl|NCBI__GCF_002019605.1:WP_078430191.1 226 GAGVLHAHAYDELFEYAEKMRIPVASTLLGLGAFPGENELFLGMAGMHGTYAANMAIHQSDLLISIGAR 294
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekiee 345
                                               fddr tg l++fap+aki hididPaeigkn++++ip+vGdak  l+ ll++  ++ ++   Wl+++++
  lcl|NCBI__GCF_002019605.1:WP_078430191.1 295 FDDRLTGALQHFAPNAKIAHIDIDPAEIGKNIETAIPVVGDAKAALKMLLEENGAVGETGV-WLAELTK 362
                                               ****************************************************999987774.******* PP

                                 TIGR00118 346 wkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGf 414
                                               +k+ey+l+++e+ e+ikPqk+++ +++++++eaivttdvGqhqmwaaq+yk++kp++++tsgGlGtmGf
  lcl|NCBI__GCF_002019605.1:WP_078430191.1 363 MKAEYPLWYKEDGETIKPQKLMELIYEVTNGEAIVTTDVGQHQMWAAQYYKFNKPNRWVTSGGLGTMGF 431
                                               ********************************************************************* PP

                                 TIGR00118 415 GlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerys 483
                                               G+Paa+Ga+ a+p++ vv++ Gd++fqm+ qels ++++++pvki+i+nn+ lGmv+qWq+lfyeerys
  lcl|NCBI__GCF_002019605.1:WP_078430191.1 432 GFPAAIGAQFAEPDTPVVSILGDAGFQMTAQELSILQDLNLPVKIIIVNNSALGMVRQWQQLFYEERYS 500
                                               ********************************************************************* PP

                                 TIGR00118 484 etklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGaglde 552
                                               ++ +++ +p+fvklaeay vkg+ri k e+++ +l+eal++++pvl+d++v + e+v+Pm+apG+g +e
  lcl|NCBI__GCF_002019605.1:WP_078430191.1 501 NSVFNT-QPNFVKLAEAYDVKGMRIDKVEDVKGALEEALAHDGPVLMDFRVTQVENVYPMIAPGKGQHE 568
                                               *****5.************************************************************** PP

                                 TIGR00118 553 lv 554
                                               + 
  lcl|NCBI__GCF_002019605.1:WP_078430191.1 569 ME 570
                                               96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (574 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: 00:00:00.03
# Mc/sec: 9.67
//
[ok]

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

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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