Alignments for a candidate for ilvI in Salinicoccus carnicancri Crm

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Salinicoccus carnicancri Crm

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_040608728.1 C792_RS0105290 biosynthetic-type acetolactate synthase large subunit

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_000330705.1:WP_040608728.1
          Length = 571

 Score =  530 bits (1365), Expect = e-155
 Identities = 283/567 (49%), Positives = 369/567 (65%), Gaps = 12/567 (2%)

Query: 39  TGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKK-LRHVLVRHEQGAGHAASGYAH 97
           TGA   I SL E GVD +FG PGGAVLP+YD L  ++   +H+L RHEQG  HAA GYA 
Sbjct: 12  TGADLFIESLVEQGVDTVFGYPGGAVLPIYDALHRAEAPFQHILCRHEQGLIHAAEGYAR 71

Query: 98  VTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGITM 157
           VTG+ GV +ATSGPGATNLVT + DA MDS+PVV  TGQV   +IG+DAFQEAD+ G+T 
Sbjct: 72  VTGKPGVVIATSGPGATNLVTGITDAMMDSLPVVVFTGQVSTAVIGSDAFQEADVIGVTT 131

Query: 158 PITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRMELPGY 217
           PITKHN+ V    ++PR++  AFHIA +GRPG V+VDIPK++ Q     ++     LPGY
Sbjct: 132 PITKHNYQVTDLKELPRIINAAFHIATTGRPGPVVVDIPKNIAQEISGETFSGDFHLPGY 191

Query: 218 KPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLMARG 277
           +P  +P+  Q+R  A  +A+A++PVL  G GV    A  +L E AE   +PV TTL+  G
Sbjct: 192 QPTYRPNPLQIRRLADALASAKRPVLLAGAGVNFSGADGELLEFAEKHRLPVTTTLLGIG 251

Query: 278 AFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKVIHADI 337
           +FP  HRQ LGM GMHG+ AA  A+  +DLLI +G RFDDR+TG L  FAPEAKV H DI
Sbjct: 252 SFPGGHRQALGMAGMHGSYAANMAIYEADLLINIGARFDDRLTGALQHFAPEAKVAHVDI 311

Query: 338 DPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADWWAYLNGVRKTYPLSYG 397
           DPAEIGKN   D+P+VGD K    E +  L   HI    +  +W++ +   + + P  + 
Sbjct: 312 DPAEIGKNVETDIPVVGDAK----EALQGLLETHIE-KADCTEWYSRVMDNKDSSPFWF- 365

Query: 398 PQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGLGTMGF 457
            +SD  +SP+++IE+L       A+    VGQHQMWAAQF ++ +P  W+ SGGLGTMGF
Sbjct: 366 ERSDELISPQWLIEELHRETDGQAIVTTDVGQHQMWAAQFYQFNEPHKWVTSGGLGTMGF 425

Query: 458 AIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGMVRQWQ 517
            +PAA+GA++  P   V +I GDG FQMT QELA      +P+KV ++NN  LGMVRQWQ
Sbjct: 426 GLPAAIGAQLGRPRETVVSIVGDGGFQMTMQELAVIKQHRLPIKVIIVNNEALGMVRQWQ 485

Query: 518 SLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQARAINDCPVVI 577
             FY ERYS + +  +    PDFVKLAE  G  G+R   E +V  V+N+  +  D PV++
Sbjct: 486 EKFYEERYSSSLMTEN----PDFVKLAEGFGIRGIRVSNEAEVPAVVNEIFSY-DGPVLV 540

Query: 578 DFIVGADAQVWPMVAAGTSNDEIQAAR 604
           D  V    +V+PMVA G  N E+   R
Sbjct: 541 DARVQKLDKVFPMVAPGKGNHEMLGVR 567


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: 1071
Number of extensions: 64
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: 571
Length adjustment: 37
Effective length of query: 581
Effective length of database: 534
Effective search space:   310254
Effective search space used:   310254
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_040608728.1 C792_RS0105290 (biosynthetic-type acetolactate synthase large 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.2007901.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-256  837.1   0.1   3.6e-256  836.9   0.1    1.0  1  NCBI__GCF_000330705.1:WP_040608728.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000330705.1:WP_040608728.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  836.9   0.1  3.6e-256  3.6e-256       2     555 ..      12     565 ..      11     567 .. 0.99

  Alignments for each domain:
  == domain 1  score: 836.9 bits;  conditional E-value: 3.6e-256
                             TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly..dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 
                                           +ga++++esl ++gv+tvfGyPGGavlpiydal+  +  ++hil rheq+ +haa+Gyar++Gk+Gvv+atsG
  NCBI__GCF_000330705.1:WP_040608728.1  12 TGADLFIESLVEQGVDTVFGYPGGAVLPIYDALHraEAPFQHILCRHEQGLIHAAEGYARVTGKPGVVIATSG 84 
                                           79********************************877789********************************* PP

                             TIGR00118  73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeia 145
                                           PGatnlvtgi++a++ds+P+vv+tGqv+t++iGsdafqe+d++G+t p+tkh+++v++ ++lp+i+++af+ia
  NCBI__GCF_000330705.1:WP_040608728.1  85 PGATNLVTGITDAMMDSLPVVVFTGQVSTAVIGSDAFQEADVIGVTTPITKHNYQVTDLKELPRIINAAFHIA 157
                                           ************************************************************************* PP

                             TIGR00118 146 stGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaease 218
                                           +tGrPGPv+vd+Pk+++++    + + + +lpgy+pt ++++lqi+++++++++ak+Pvll+G+Gv  ++a+ 
  NCBI__GCF_000330705.1:WP_040608728.1 158 TTGRPGPVVVDIPKNIAQEISGETFSGDFHLPGYQPTYRPNPLQIRRLADALASAKRPVLLAGAGVNFSGADG 230
                                           ************************************************************************* PP

                             TIGR00118 219 elkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfape 291
                                           el e+ae+ ++pvtttllG+G+fp  h++algm+GmhG+++an+a+ eadlli +Garfddr tg l++fape
  NCBI__GCF_000330705.1:WP_040608728.1 231 ELLEFAEKHRLPVTTTLLGIGSFPGGHRQALGMAGMHGSYAANMAIYEADLLINIGARFDDRLTGALQHFAPE 303
                                           ************************************************************************* PP

                             TIGR00118 292 akiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPq 364
                                           ak+ h+didPaeigknv++dip+vGdak+ l+ ll++  e+ + + eW++++ + k+++++++++++e i Pq
  NCBI__GCF_000330705.1:WP_040608728.1 304 AKVAHVDIDPAEIGKNVETDIPVVGDAKEALQGLLETHIEKADCT-EWYSRVMDNKDSSPFWFERSDELISPQ 375
                                           ************************************998887666.6************************** PP

                             TIGR00118 365 kvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGd 437
                                            +i+el++ ++++aivttdvGqhqmwaaqfy++++p+k++tsgGlGtmGfGlPaa+Ga+++ p etvv+++Gd
  NCBI__GCF_000330705.1:WP_040608728.1 376 WLIEELHRETDGQAIVTTDVGQHQMWAAQFYQFNEPHKWVTSGGLGTMGFGLPAAIGAQLGRPRETVVSIVGD 448
                                           ************************************************************************* PP

                             TIGR00118 438 gsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriek 510
                                           g+fqm++qel++i++  +p+k++i+nne lGmv+qWqe fyeerys++ ++ e+pdfvklae++G++gir+++
  NCBI__GCF_000330705.1:WP_040608728.1 449 GGFQMTMQELAVIKQHRLPIKVIIVNNEALGMVRQWQEKFYEERYSSSLMT-ENPDFVKLAEGFGIRGIRVSN 520
                                           **************************************************9.7******************** PP

                             TIGR00118 511 peeleeklkealeskepvlldvevdkeeevlPmvapGagldelve 555
                                           ++e+ + ++e+++ ++pvl+d +v+k ++v+PmvapG+g++e+++
  NCBI__GCF_000330705.1:WP_040608728.1 521 EAEVPAVVNEIFSYDGPVLVDARVQKLDKVFPMVAPGKGNHEMLG 565
                                           *******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (571 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: 0.01u 0.02s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 9.19
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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