GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Lentibacillus jeotgali Grbi

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_010532006.1 ON01_RS15950 biosynthetic-type acetolactate synthase large subunit

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_000224785.1:WP_010532006.1
          Length = 575

 Score =  521 bits (1341), Expect = e-152
 Identities = 273/570 (47%), Positives = 371/570 (65%), Gaps = 18/570 (3%)

Query: 36  QQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKK-LRHVLVRHEQGAGHAASG 94
           +++TGA  +I++L  + VD +FG PGGAVLP+YD L+ S    +HVL RHEQGA HAA G
Sbjct: 14  KKVTGADLLIQTLTAVNVDTVFGYPGGAVLPIYDALYRSDAPFKHVLTRHEQGAAHAAEG 73

Query: 95  YAHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISG 154
           YA VTG+ GV +ATSGPGATNL+T + DA MDS+P+V  TGQV   +IGTDAFQE+D+ G
Sbjct: 74  YARVTGKPGVVLATSGPGATNLITGITDAMMDSLPMVVFTGQVASNVIGTDAFQESDVMG 133

Query: 155 ITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRME- 213
           IT P+TK+N+ VR   ++PR++ EAFHIA++GRPG V+VDIPKD+       S     + 
Sbjct: 134 ITTPVTKYNYQVRDLKELPRIVKEAFHIASTGRPGPVVVDIPKDISSTVSGISVELNDDC 193

Query: 214 -LPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTT 272
            LPGY+PN KP+  Q+ + A+ I+ A+KP++  G GV+  EA+++L   AE   +PVV T
Sbjct: 194 YLPGYQPNKKPNPLQIVKLAEAISRAKKPLILAGAGVVSAEASKELTAFAEKHKLPVVNT 253

Query: 273 LMARGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKV 332
           L+  G F  +H  +LGM GMHG  AA   +   DLLI +G RFDDR+TG L  FAP AKV
Sbjct: 254 LLGLGGFSGTHELSLGMGGMHGCYAANQGVYECDLLINIGARFDDRLTGNLKHFAPNAKV 313

Query: 333 IHADIDPAEIGKNRHADVPIVGDVKAVITELI--AMLRHHHIPGTIEMADWWAYLNGVRK 390
            H DIDPAEIGKN   ++P+V D K  +  L+   +  + H        DW   L   + 
Sbjct: 314 AHVDIDPAEIGKNVETEIPVVADAKEALEALVKTEITANDH-------GDWLDTLRQNQM 366

Query: 391 TYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSG 450
            YP  Y  +S+  +SP+++ E++ +++  +A+    VGQHQMWAAQ+  +  P  W+ SG
Sbjct: 367 DYPYWY-DRSETYISPQWLTEQIYKVSDGEAIVTTDVGQHQMWAAQYYPFANPNKWVTSG 425

Query: 451 GLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNL 510
           GLGTMGF  PAA+GA++  P   V A+ GDG FQMT QEL+      +PVKV ++NN +L
Sbjct: 426 GLGTMGFGFPAAVGAQLGAPDELVVAVVGDGGFQMTAQELSVIKERQLPVKVVIVNNQSL 485

Query: 511 GMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQARAI 570
           GMVRQWQ  FY +RYS++    +    PDFVKLAE  G +G+R E E ++ DV+  A   
Sbjct: 486 GMVRQWQEKFYDKRYSESIFPEN----PDFVKLAECYGILGMRAENESELPDVLTDAFNY 541

Query: 571 NDCPVVIDFIVGADAQVWPMVAAGTSNDEI 600
            D PVVID  V  +  V+PM+A G    E+
Sbjct: 542 -DGPVVIDCHVVQEECVYPMIAPGKGMHEM 570


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: 1059
Number of extensions: 43
Number of successful extensions: 6
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: 575
Length adjustment: 37
Effective length of query: 581
Effective length of database: 538
Effective search space:   312578
Effective search space used:   312578
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_010532006.1 ON01_RS15950 (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.3245558.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.9e-254  830.6   0.3   3.3e-254  830.4   0.3    1.0  1  NCBI__GCF_000224785.1:WP_010532006.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_010532006.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  830.4   0.3  3.3e-254  3.3e-254       2     556 ..      17     573 ..      16     574 .. 0.98

  Alignments for each domain:
  == domain 1  score: 830.4 bits;  conditional E-value: 3.3e-254
                             TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly..dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 
                                           +ga++l+++l++ +v+tvfGyPGGavlpiydaly  d  ++h+l+rheq+aahaa+Gyar++Gk+GvvlatsG
  NCBI__GCF_000224785.1:WP_010532006.1  17 TGADLLIQTLTAVNVDTVFGYPGGAVLPIYDALYrsDAPFKHVLTRHEQGAAHAAEGYARVTGKPGVVLATSG 89 
                                           79********************************766679********************************* PP

                             TIGR00118  73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeia 145
                                           PGatnl+tgi++a++ds+P+vv+tGqva+++iG+dafqe d++Git pvtk++++v++ ++lp+i+keaf+ia
  NCBI__GCF_000224785.1:WP_010532006.1  90 PGATNLITGITDAMMDSLPMVVFTGQVASNVIGTDAFQESDVMGITTPVTKYNYQVRDLKELPRIVKEAFHIA 162
                                           ************************************************************************* PP

                             TIGR00118 146 stGrPGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaea 216
                                           stGrPGPv+vd+Pkd++++   ++ve  ++  lpgy+p++k+++lqi k++e+i++akkP++l+G+Gv+ aea
  NCBI__GCF_000224785.1:WP_010532006.1 163 STGRPGPVVVDIPKDISSTVSGISVElnDDCYLPGYQPNKKPNPLQIVKLAEAISRAKKPLILAGAGVVSAEA 235
                                           ****************9887655555549******************************************** PP

                             TIGR00118 217 seelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfa 289
                                           s+el+ +ae+ k+pv+ tllGlG+f  +h+l+lgm GmhG+++an  v e+dlli +Garfddr tgnl++fa
  NCBI__GCF_000224785.1:WP_010532006.1 236 SKELTAFAEKHKLPVVNTLLGLGGFSGTHELSLGMGGMHGCYAANQGVYECDLLINIGARFDDRLTGNLKHFA 308
                                           ************************************************************************* PP

                             TIGR00118 290 peakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesik 362
                                           p+ak+ h+didPaeigknv+++ip+v dak+ le l+k+  + +++  +Wl+ +++ + +y++++d++e+ i 
  NCBI__GCF_000224785.1:WP_010532006.1 309 PNAKVAHVDIDPAEIGKNVETEIPVVADAKEALEALVKTEITANDHG-DWLDTLRQNQMDYPYWYDRSETYIS 380
                                           *************************************9988887776.6************************ PP

                             TIGR00118 363 PqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavt 435
                                           Pq + ++++k+ ++eaivttdvGqhqmwaaq+y++ +p+k++tsgGlGtmGfG+Paa+Ga+++ p+e vvav+
  NCBI__GCF_000224785.1:WP_010532006.1 381 PQWLTEQIYKVSDGEAIVTTDVGQHQMWAAQYYPFANPNKWVTSGGLGTMGFGFPAAVGAQLGAPDELVVAVV 453
                                           ************************************************************************* PP

                             TIGR00118 436 GdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiri 508
                                           Gdg+fqm+ qels+i+e ++pvk+vi+nn+ lGmv+qWqe fy++ryse+ +  e+pdfvklae+yG+ g+r 
  NCBI__GCF_000224785.1:WP_010532006.1 454 GDGGFQMTAQELSVIKERQLPVKVVIVNNQSLGMVRQWQEKFYDKRYSESIFP-ENPDFVKLAECYGILGMRA 525
                                           ****************************************************9.7****************** PP

                             TIGR00118 509 ekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelvee 556
                                           e+++el + l++a++ ++pv++d +v +ee v+Pm+apG+g++e++++
  NCBI__GCF_000224785.1:WP_010532006.1 526 ENESELPDVLTDAFNYDGPVVIDCHVVQEECVYPMIAPGKGMHEMIGV 573
                                           *********************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (575 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 35.63
//
[ok]

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

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:

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:

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:

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