Alignments for a candidate for ilvI in Desulfobulbus mediterraneus DSM 13871

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Desulfobulbus mediterraneus DSM 13871

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_028582963.1 G494_RS0100685 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000429965.1:WP_028582963.1
          Length = 566

 Score =  588 bits (1517), Expect = e-172
 Identities = 303/563 (53%), Positives = 392/563 (69%), Gaps = 6/563 (1%)

Query: 21  GAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYARAT 80
           G++ ++  L EEGVE ++GYPGGAV+ +YD+L K T  +H+LVRHEQ AVHAADG+ARAT
Sbjct: 6   GSQAIIKCLQEEGVELLFGYPGGAVIELYDQLCKST-IKHVLVRHEQGAVHAADGFARAT 64

Query: 81  GKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITRPI 140
           GKVGVA++TSGPG TN VT IATAY DSIP+VV+TG VP   IG DAFQE D VGITRP 
Sbjct: 65  GKVGVAVLTSGPGATNGVTAIATAYCDSIPLVVLTGQVPRPLIGNDAFQEVDIVGITRPC 124

Query: 141 VKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRSYNP 200
            KHN+LV D   L   +++AF++AA+GRPGPV+VD+PKDV      Y   + I + +Y P
Sbjct: 125 TKHNYLVSDPDQLVPILREAFYLAASGRPGPVLVDLPKDVIAALIDYPEKRPIKIPTYQP 184

Query: 201 VNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGLGAF 260
                 GQ+ KA      AE+P +Y GGGV+LA+ + EL +LA     PVT TLMGLGAF
Sbjct: 185 NTTPDPGQVEKACRACLKAEKPVLYVGGGVILADGNQELTRLARELNIPVTMTLMGLGAF 244

Query: 261 PGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHIDID 320
           PG+ +  +GMLGMHG+Y ANM++   D+LIA+GARFDDRV G    F   A  IIHIDID
Sbjct: 245 PGSDELSLGMLGMHGSYAANMSVAKSDLLIAVGARFDDRVTGKLEAFAPHA-DIIHIDID 303

Query: 321 PSSISKRVKVDIPIVGNVKDVLQELIA---QIKASDIKPKREALAKWWEQIEQWRSVDCL 377
           P+SISK ++VDIPIV + ++ LQ +++   + +  ++K        W EQ+ +W     L
Sbjct: 304 PTSISKNIEVDIPIVADCREALQAMLSWLEEYRELNLKEVATRHRPWVEQVREWDRKHPL 363

Query: 378 KYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437
            Y    +IIKPQYV+E I ELT G+A I ++VGQ+QMWAAQFY F++PRR + SGGLGTM
Sbjct: 364 SYHDEGQIIKPQYVIETINELTGGNAIITTEVGQNQMWAAQFYTFNQPRRLLTSGGLGTM 423

Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497
           G GLP A+G + AFP+  V  I G+GSIQM IQEL+T  QY  PVK+  LNN +LGMVRQ
Sbjct: 424 GYGLPAAIGAQFAFPDLPVFDIAGDGSIQMNIQELATAKQYGIPVKVAILNNKFLGMVRQ 483

Query: 498 WQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDF 557
           WQE+ YD  Y+ + M+  PDFV+LA+A+G VG+R     +V P ++EA    D +V +DF
Sbjct: 484 WQELFYDRHYASTAMEYTPDFVELAKAFGAVGLRATTKDEVRPVIQEALD-TDNSVLMDF 542

Query: 558 QTDPTENVWPMVQAGKGISEMLL 580
                E V+PMV AGK  +EMLL
Sbjct: 543 SISREEGVFPMVPAGKANTEMLL 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: 916
Number of extensions: 41
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: 566
Length adjustment: 36
Effective length of query: 549
Effective length of database: 530
Effective search space:   290970
Effective search space used:   290970
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_028582963.1 G494_RS0100685 (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.31964.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.1e-250  817.3   0.0   3.5e-250  817.1   0.0    1.0  1  lcl|NCBI__GCF_000429965.1:WP_028582963.1  G494_RS0100685 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429965.1:WP_028582963.1  G494_RS0100685 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  817.1   0.0  3.5e-250  3.5e-250       3     554 ..       6     564 ..       4     566 .] 0.98

  Alignments for each domain:
  == domain 1  score: 817.1 bits;  conditional E-value: 3.5e-250
                                 TIGR00118   3 gaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlats 71 
                                               g++++++ l++egve +fGyPGGav+++yd+l +s ++h+lvrheq+a+haadG+ara+GkvGv++ ts
  lcl|NCBI__GCF_000429965.1:WP_028582963.1   6 GSQAIIKCLQEEGVELLFGYPGGAVIELYDQLCKSTIKHVLVRHEQGAVHAADGFARATGKVGVAVLTS 74 
                                               899****************************************************************** PP

                                 TIGR00118  72 GPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilke 140
                                               GPGatn vt+iatay ds+PlvvltGqv++ liG+dafqe+di+Git+p+tkh++lv+++++l  il+e
  lcl|NCBI__GCF_000429965.1:WP_028582963.1  75 GPGATNGVTAIATAYCDSIPLVVLTGQVPRPLIGNDAFQEVDIVGITRPCTKHNYLVSDPDQLVPILRE 143
                                               ********************************************************************* PP

                                 TIGR00118 141 afeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGg 209
                                               af++a++GrPGPvlvdlPkdv +a i+++ ++ +++p+y+p++++++ q++ka  +  ka+kPvl+vGg
  lcl|NCBI__GCF_000429965.1:WP_028582963.1 144 AFYLAASGRPGPVLVDLPKDVIAALIDYPEKRPIKIPTYQPNTTPDPGQVEKACRACLKAEKPVLYVGG 212
                                               ********************************************************************* PP

                                 TIGR00118 210 GviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfd 278
                                               Gvi a++++el++la +l+ipvt+tl+GlGafp  ++l+lgmlGmhG+++an++v ++dlliavGarfd
  lcl|NCBI__GCF_000429965.1:WP_028582963.1 213 GVILADGNQELTRLARELNIPVTMTLMGLGAFPGSDELSLGMLGMHGSYAANMSVAKSDLLIAVGARFD 281
                                               ********************************************************************* PP

                                 TIGR00118 279 drvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee........ekkeke. 338
                                               drvtg+l+ fap+a iihididP++i+kn++vdipiv d+++ l+ +l+ l+e+         ++ ++ 
  lcl|NCBI__GCF_000429965.1:WP_028582963.1 282 DRVTGKLEAFAPHADIIHIDIDPTSISKNIEVDIPIVADCREALQAMLSWLEEYrelnlkevATR-HRp 349
                                               *************************************************9998877877653333.346 PP

                                 TIGR00118 339 WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsg 407
                                               W+e+++ew ++++l+++ e + ikPq+vi+++ +l+ ++ai+tt+vGq+qmwaaqfy++++pr+ +tsg
  lcl|NCBI__GCF_000429965.1:WP_028582963.1 350 WVEQVREWDRKHPLSYHDEGQIIKPQYVIETINELTGGNAIITTEVGQNQMWAAQFYTFNQPRRLLTSG 418
                                               ********************************************************************* PP

                                 TIGR00118 408 GlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqel 476
                                               GlGtmG+GlPaa+Ga+ a p+  v +++Gdgs+qmn+qel+t+++y+ipvk+ ilnn++lGmv+qWqel
  lcl|NCBI__GCF_000429965.1:WP_028582963.1 419 GLGTMGYGLPAAIGAQFAFPDLPVFDIAGDGSIQMNIQELATAKQYGIPVKVAILNNKFLGMVRQWQEL 487
                                               ********************************************************************* PP

                                 TIGR00118 477 fyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmva 545
                                               fy++ y++t ++  +pdfv+la+a+G++g+r ++++e+   ++eal +++ vl+d+++ +ee v+Pmv+
  lcl|NCBI__GCF_000429965.1:WP_028582963.1 488 FYDRHYASTAMEY-TPDFVELAKAFGAVGLRATTKDEVRPVIQEALDTDNSVLMDFSISREEGVFPMVP 555
                                               ************6.******************************************************* PP

                                 TIGR00118 546 pGagldelv 554
                                                G++++e++
  lcl|NCBI__GCF_000429965.1:WP_028582963.1 556 AGKANTEML 564
                                               *******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (566 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 12.83
//
[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