Alignments for a candidate for ilvI in Desulfovibrio gracilis DSM 16080

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Desulfovibrio gracilis DSM 16080

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_078717001.1 B5D49_RS07175 acetolactate synthase, large subunit, biosynthetic type

Query= SwissProt::P0DP90
         (548 letters)



>NCBI__GCF_900167125.1:WP_078717001.1
          Length = 564

 Score =  480 bits (1235), Expect = e-140
 Identities = 258/554 (46%), Positives = 349/554 (62%), Gaps = 12/554 (2%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGV-EHLLCRHEQGAAMAAIGYAR 59
           M GA+ ++  L  QG+ T+ G PGGA +P+YDAL    V  H+L RHEQGA   A G AR
Sbjct: 4   MTGAEILIRLLERQGIQTIPGIPGGANLPLYDALSRSPVIRHVLARHEQGAGFMAQGMAR 63

Query: 60  ATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSL 119
            TGK  V  ATSGPGATN +T LADA LDS+PV+ ITGQV +  IGTDAFQEVD+ G+S+
Sbjct: 64  VTGKPQVFFATSGPGATNTLTALADAKLDSVPVICITGQVPSAMIGTDAFQEVDIYGMSI 123

Query: 120 ACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDL----EPWFTTV 175
             TKH+FLV+S+EEL +++ EAF +A SGRPGPVLVDIPKD+Q    D+    EP     
Sbjct: 124 PATKHNFLVRSVEELLQVIPEAFRIAASGRPGPVLVDIPKDVQTGELDMTSWPEPGLPDA 183

Query: 176 ENEVTFPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLG 235
              V   H  V +A  M+ +A++P+LY+GGGV  + A P  +       +P   TL GLG
Sbjct: 184 PQAVESEH--VNRAAAMINEAKRPILYLGGGVIQSGAAPLAKNLAELAGIPTVMTLMGLG 241

Query: 236 AVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMDI 295
           A+ +D+P  LGMLGMH    AN A++ECDLLIA G RFDDR TGK+  F P A +IHMDI
Sbjct: 242 AMPSDHPLSLGMLGMHAAPCANLALEECDLLIAAGVRFDDRATGKVEQFCPGAKIIHMDI 301

Query: 296 DPAEMNKLRQAHVALQGDL----NALLPALQQPLNQYDWQQHCAQLRDEHSWRYDHPGDA 351
           DPAE+ K+R AH A+ GD+     +L+P ++       W +   +L+ EHS   +   + 
Sbjct: 302 DPAELGKIRPAHQAMVGDVGQAFQSLIPHIRAG-KPGQWLERVHELKTEHSMYLEDAENV 360

Query: 352 IYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAV 411
           +    ++ + +       VV TDVGQHQM  AQ      P  ++TS GLGTMGFGLPAA+
Sbjct: 361 LSGYGIVLETARAVGRGAVVVTDVGQHQMRTAQAYPLDTPRRWLTSGGLGTMGFGLPAAI 420

Query: 412 GAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQE 471
           GA +ARP+  VVC SGDGS +MN+QE+ T   +   +K+VL +N  LG+VRQ Q+LF+  
Sbjct: 421 GAALARPDLPVVCFSGDGSLLMNLQEMATAVEQGTNVKLVLTNNNALGLVRQQQELFYSG 480

Query: 472 RYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDELENVW 531
               +    + DF+ +A  FG +  ++         L   L   GP L+H++++  +NV+
Sbjct: 481 NLFASGYEYSVDFMQIARGFGWNTVNLDDSADPAEDLREALARTGPGLIHLTVNPGQNVF 540

Query: 532 PLVPPGASNSEMLE 545
           P+VPPGA+N EM+E
Sbjct: 541 PMVPPGAANKEMIE 554


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: 874
Number of extensions: 46
Number of successful extensions: 4
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: 564
Length adjustment: 36
Effective length of query: 512
Effective length of database: 528
Effective search space:   270336
Effective search space used:   270336
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_078717001.1 B5D49_RS07175 (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.29599.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-201  656.6   0.0   1.7e-201  656.4   0.0    1.0  1  lcl|NCBI__GCF_900167125.1:WP_078717001.1  B5D49_RS07175 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900167125.1:WP_078717001.1  B5D49_RS07175 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  656.4   0.0  1.7e-201  1.7e-201       1     556 [.       4     555 ..       4     556 .. 0.98

  Alignments for each domain:
  == domain 1  score: 656.4 bits;  conditional E-value: 1.7e-201
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               ++gaeil++ l+++g++t+ G+PGGa lp+ydal  +  ++h+l+rheq+a  +a+G+ar++Gk+ v +
  lcl|NCBI__GCF_900167125.1:WP_078717001.1   4 MTGAEILIRLLERQGIQTIPGIPGGANLPLYDALSrSPVIRHVLARHEQGAGFMAQGMARVTGKPQVFF 72 
                                               79*********************************67789***************************** PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               atsGPGatn++t++a+a ldsvP++ +tGqv++++iG+dafqe+di G+++p tkh+flv+++e+l ++
  lcl|NCBI__GCF_900167125.1:WP_078717001.1  73 ATSGPGATNTLTALADAKLDSVPVICITGQVPSAMIGTDAFQEVDIYGMSIPATKHNFLVRSVEELLQV 141
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206
                                               + eaf ia++GrPGPvlvd+Pkdv++ e++++   +  lp     v++    +++a+ +i++ak+P+l+
  lcl|NCBI__GCF_900167125.1:WP_078717001.1 142 IPEAFRIAASGRPGPVLVDIPKDVQTGELDMTSWPEPGLPDAPQAVES--EHVNRAAAMINEAKRPILY 208
                                               **********************************9*****87666654..579**************** PP

                                 TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275
                                                GgGvi+++a    k+lae + ip ++tl+GlGa+p+dhpl+lgmlGmh +  anla++e+dllia G+
  lcl|NCBI__GCF_900167125.1:WP_078717001.1 209 LGGGVIQSGAAPLAKNLAELAGIPTVMTLMGLGAMPSDHPLSLGMLGMHAAPCANLALEECDLLIAAGV 277
                                               ********************************************************************* PP

                                 TIGR00118 276 rfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekie 344
                                               rfddr tg++++f+p akiih+didPae+gk++ ++ ++vGd+ + ++ l+ ++++ +  +  Wle+++
  lcl|NCBI__GCF_900167125.1:WP_078717001.1 278 RFDDRATGKVEQFCPGAKIIHMDIDPAELGKIRPAHQAMVGDVGQAFQSLIPHIRAGKPGQ--WLERVH 344
                                               ******************************************************9988777..****** PP

                                 TIGR00118 345 ewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmG 413
                                               e+k+e+ + l+  e+ +    ++ e  + +   a+v tdvGqhqm +aq y+ ++pr+++tsgGlGtmG
  lcl|NCBI__GCF_900167125.1:WP_078717001.1 345 ELKTEHSMYLEDAENVLSGYGIVLETARAVGRGAVVVTDVGQHQMRTAQAYPLDTPRRWLTSGGLGTMG 413
                                               ****************************99999************************************ PP

                                 TIGR00118 414 fGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeery 482
                                               fGlPaa+Ga +a p+  vv+ +Gdgs+ mnlqe++t+ve +++vk+v+ nn+ lG+v+q qelfy++  
  lcl|NCBI__GCF_900167125.1:WP_078717001.1 414 FGLPAAIGAALARPDLPVVCFSGDGSLLMNLQEMATAVEQGTNVKLVLTNNNALGLVRQQQELFYSGNL 482
                                               ********************************************************************* PP

                                 TIGR00118 483 setklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagld 551
                                                ++  +  + df+++a+++G +++++ + ++ +e l+eal+ ++p l+ ++v+  ++v+Pmv+pGa+++
  lcl|NCBI__GCF_900167125.1:WP_078717001.1 483 FASGYEY-SVDFMQIARGFGWNTVNLDDSADPAEDLREALARTGPGLIHLTVNPGQNVFPMVPPGAANK 550
                                               *999995.99*********************************************************** PP

                                 TIGR00118 552 elvee 556
                                               e++e 
  lcl|NCBI__GCF_900167125.1:WP_078717001.1 551 EMIEA 555
                                               **985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (564 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: 00:00:00.08
# Mc/sec: 3.64
//
[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