Alignments for a candidate for ilvI in Sedimenticola selenatireducens DSM 17993

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Sedimenticola selenatireducens DSM 17993

Align Acetolactate synthase isozyme 2 large subunit; AHAS-II; ALS-II; Acetohydroxy-acid synthase II large subunit; EC 2.2.1.6 (characterized)
to candidate WP_051302371.1 A3GO_RS0114660 acetolactate synthase 2 catalytic subunit

Query= SwissProt::P0DP90
         (548 letters)



>NCBI__GCF_000428045.1:WP_051302371.1
          Length = 565

 Score =  595 bits (1535), Expect = e-174
 Identities = 300/547 (54%), Positives = 389/547 (71%), Gaps = 5/547 (0%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARA 60
           MNGA+++V  L ++GV+T+FGYPGG +MP+YDAL +  + H+LCRHEQG A AA GYAR+
Sbjct: 16  MNGAEYIVRKLISEGVDTLFGYPGGCVMPLYDALLESPIRHILCRHEQGTAFAANGYARS 75

Query: 61  TGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLA 120
           +G+ GVC+ATSGPGATNL+TGLADA +DS+P+VAITGQV    IGTDAFQE+DVLG+SL 
Sbjct: 76  SGRIGVCLATSGPGATNLMTGLADAYMDSVPMVAITGQVPTALIGTDAFQEIDVLGMSLP 135

Query: 121 CTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENE-- 178
            TK SFLVQ+++ELP I+ +AF +A  GRPGPVLVD+PKDIQLA+   EP    +  E  
Sbjct: 136 ITKQSFLVQAIDELPEILDQAFRIALEGRPGPVLVDLPKDIQLATLS-EPTIPHLSGERI 194

Query: 179 -VTFPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAV 237
             T   A+ +QA +++  +++P++Y GGG+ +  AV   R+F+  T +PA  +LKGLGA+
Sbjct: 195 SNTTTPAQWQQAIELMNTSRRPIIYGGGGILLGDAVSPFRQFVETTGIPAVFSLKGLGAL 254

Query: 238 EADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDIDP 297
             D+P  +GMLGMHG+ AAN  VQE DLLIAVG RFDDRVTGKL+ FAPHA VIH+DIDP
Sbjct: 255 PGDHPLNMGMLGMHGSVAANQVVQEADLLIAVGVRFDDRVTGKLSRFAPHAQVIHLDIDP 314

Query: 298 AEMNKLRQAHVALQGDLNALLPALQQPLNQYDWQQHCAQLRDEHSWRYDHPGDAIYAPLL 357
           AE+ KLRQA  AL GD+   L AL   LN  DWQ  C +  ++  +      D I  P  
Sbjct: 315 AEIGKLRQAVCALPGDIKQSLKALTIKLNLLDWQSQCLERLEQDGFALP-AQDGITGPHF 373

Query: 358 LKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVGAQVAR 417
           ++ LS       +++ DVGQHQMW AQH A   P   +TS GLG MGFGLPAA+GAQ+A 
Sbjct: 374 MRLLSQTTRGQAIISCDVGQHQMWVAQHYAFDHPRKHLTSGGLGAMGFGLPAAIGAQLAN 433

Query: 418 PNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYSETT 477
               V+ ++GDGSFMMN QEL T+ R +LP KI++LDNQ LGMVRQ Q + +Q RYSE  
Sbjct: 434 SEIPVINVAGDGSFMMNAQELATIGRYRLPTKIIILDNQALGMVRQQQSVCYQGRYSEID 493

Query: 478 LTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVWPLVPPG 537
           L+DNPDF  LA AFGI  Q I+  D +  A++ +L + GP LLHV+I    NVWP+V PG
Sbjct: 494 LSDNPDFCTLARAFGIPAQSISDPDDMAYAINKLLETPGPALLHVAIATEHNVWPMVKPG 553

Query: 538 ASNSEML 544
            +N +++
Sbjct: 554 DANDQII 560


Lambda     K      H
   0.320    0.135    0.410 

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: 937
Number of extensions: 39
Number of successful extensions: 3
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: 548
Length of database: 565
Length adjustment: 36
Effective length of query: 512
Effective length of database: 529
Effective search space:   270848
Effective search space used:   270848
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_051302371.1 A3GO_RS0114660 (acetolactate synthase 2 catalytic 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.8788.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.5e-212  691.7   0.0   4.1e-212  691.5   0.0    1.0  1  lcl|NCBI__GCF_000428045.1:WP_051302371.1  A3GO_RS0114660 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000428045.1:WP_051302371.1  A3GO_RS0114660 acetolactate synthase 2 catalytic subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  691.5   0.0  4.1e-212  4.1e-212       1     555 [.      16     561 ..      16     563 .. 0.96

  Alignments for each domain:
  == domain 1  score: 691.5 bits;  conditional E-value: 4.1e-212
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               ++gae +v+ l +egv+t+fGyPGG v+p+ydal +s ++hil rheq++a aa+Gyar+sG++Gv+la
  lcl|NCBI__GCF_000428045.1:WP_051302371.1  16 MNGAEYIVRKLISEGVDTLFGYPGGCVMPLYDALLESPIRHILCRHEQGTAFAANGYARSSGRIGVCLA 84 
                                               78******************************************************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatnl+tg+a+ay+dsvP+v++tGqv+t+liG+dafqeid+lG++lp+tk sflv+  ++lpeil
  lcl|NCBI__GCF_000428045.1:WP_051302371.1  85 TSGPGATNLMTGLADAYMDSVPMVAITGQVPTALIGTDAFQEIDVLGMSLPITKQSFLVQAIDELPEIL 153
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                                +af ia  GrPGPvlvdlPkd++ a+++ ++    +l g +   ++ ++q ++a+el++++++P+++ 
  lcl|NCBI__GCF_000428045.1:WP_051302371.1 154 DQAFRIALEGRPGPVLVDLPKDIQLATLSEPTI--PHLSGERISNTTTPAQWQQAIELMNTSRRPIIYG 220
                                               *************************99988876..6899****************************** PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgG++ ++a   +++++e++ ip + +l GlGa+p dhpl +gmlGmhG+ +an  v+eadlliavG+r
  lcl|NCBI__GCF_000428045.1:WP_051302371.1 221 GGGILLGDAVSPFRQFVETTGIPAVFSLKGLGALPGDHPLNMGMLGMHGSVAANQVVQEADLLIAVGVR 289
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekiee 345
                                               fddrvtg+l++fap+a++ih+didPaeigk +++  ++ Gd k+ l+ l  kl+  +     W ++  e
  lcl|NCBI__GCF_000428045.1:WP_051302371.1 290 FDDRVTGKLSRFAPHAQVIHLDIDPAEIGKLRQAVCALPGDIKQSLKALTIKLNLLD-----WQSQCLE 353
                                               ************************************************999887765.....5555544 PP

                                 TIGR00118 346 wkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGf 414
                                                 ++  ++l  ++  i   ++++ ls+ ++++ai++ dvGqhqmw+aq+y +++prk++tsgGlG+mGf
  lcl|NCBI__GCF_000428045.1:WP_051302371.1 354 RLEQDGFALPAQD-GITGPHFMRLLSQTTRGQAIISCDVGQHQMWVAQHYAFDHPRKHLTSGGLGAMGF 421
                                               4455555677665.56666899*********************************************** PP

                                 TIGR00118 415 GlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerys 483
                                               GlPaa+Ga++a++e  v++v+Gdgsf+mn qel+ti +y +p ki+il+n+ lGmv+q q++ y++rys
  lcl|NCBI__GCF_000428045.1:WP_051302371.1 422 GLPAAIGAQLANSEIPVINVAGDGSFMMNAQELATIGRYRLPTKIIILDNQALGMVRQQQSVCYQGRYS 490
                                               ********************************************************************* PP

                                 TIGR00118 484 etklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGaglde 552
                                               e  l+ ++pdf  la+a+G+ ++ i++p++++ +++++le+ +p+ll v +++e++v+Pmv pG ++d+
  lcl|NCBI__GCF_000428045.1:WP_051302371.1 491 EIDLS-DNPDFCTLARAFGIPAQSISDPDDMAYAINKLLETPGPALLHVAIATEHNVWPMVKPGDANDQ 558
                                               ****9.6************************************************************** PP

                                 TIGR00118 553 lve 555
                                               +++
  lcl|NCBI__GCF_000428045.1:WP_051302371.1 559 IIT 561
                                               985 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 12.27
//
[ok]

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

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Steps (tab-delimited)
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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