Alignments for a candidate for ilvI in Kyrpidia tusciae DSM 2912

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Kyrpidia tusciae DSM 2912

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_013074976.1 BTUS_RS04765 acetolactate synthase large subunit

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_000092905.1:WP_013074976.1
          Length = 578

 Score =  582 bits (1501), Expect = e-170
 Identities = 305/587 (51%), Positives = 393/587 (66%), Gaps = 24/587 (4%)

Query: 14  PEPHSAANEPKHPAARPKHVALQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFD 73
           PEP ++A     PAA P+      +TGA+ ++  L+  GV+++FG PGGAVLP+YD L+ 
Sbjct: 10  PEPEASA-----PAAGPR-----VMTGAEMLVECLKREGVEIMFGYPGGAVLPIYDALYG 59

Query: 74  SKKLRHVLVRHEQGAGHAASGYAHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAI 133
           S  +RH+L RHEQGA HAA GYA VTGR GV +ATSGPGATNLVT +ADA MDS P+V  
Sbjct: 60  SG-IRHILTRHEQGAVHAAEGYARVTGRPGVVLATSGPGATNLVTGIADAYMDSTPLVLF 118

Query: 134 TGQVGRGLIGTDAFQEADISGITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLV 193
           TGQV   LIG+D+FQEADI GITMPITKH++ VR   DIPRV+ EAFHIAA+GRPG VL+
Sbjct: 119 TGQVATDLIGSDSFQEADIIGITMPITKHSYQVRDAADIPRVVREAFHIAATGRPGPVLI 178

Query: 194 DIPKDVLQGQCTFSWPPRMELPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGE 253
           D+PK+V   +  F WP R+ + GY P   P+  Q+ +  + I  +R+P+LYVGGGV+   
Sbjct: 179 DVPKNVANQKAVFEWPERVFIRGYNPTYTPNPTQLSKVTEAIRESRRPLLYVGGGVVHSG 238

Query: 254 ATEQLRELAELTGIPVVTTLMARGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGT 313
           A E+LRE A  TGIPVV+TLM  GAFP +    +GM GMHGT AA  A+   DLLIA+G 
Sbjct: 239 AAEELREFAHKTGIPVVSTLMGLGAFPSADPLFVGMLGMHGTFAANRAVMECDLLIAVGA 298

Query: 314 RFDDRVTGKLDSFAPEAKVIHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIP 373
           RFDDRVTGKL+ F+P +K +H DIDPAEIGKN   D+P+VGDVK V++ ++  +      
Sbjct: 299 RFDDRVTGKLERFSPHSKKVHIDIDPAEIGKNVAVDLPLVGDVKRVLSAMLPEV------ 352

Query: 374 GTIEMADWWAYLNGVRKTYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMW 433
           G +    W   +    + +PL Y  +  G L P+ V+E L +    +A+    VGQHQMW
Sbjct: 353 GPVGTKAWLEQIRAWDEQWPLGYKAE-PGVLKPQQVLEMLWDATQGEAILTTEVGQHQMW 411

Query: 434 AAQFIRYEKPRSWLNSGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATC 493
           AA F R++ PR W+ SGGLGTMGF  PAAMG ++A PG  V  + GD  FQM  QEL T 
Sbjct: 412 AALFYRFKHPRQWVTSGGLGTMGFGFPAAMGVQLAKPGETVICVAGDASFQMNIQELQTV 471

Query: 494 AVEGIPVKVALINNGNLGMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLR 553
           A   +PVKVA+INNG LGMVRQWQ LFY  RY+++ +       PDFVK+AEA G  GLR
Sbjct: 472 AENDLPVKVAIINNGFLGMVRQWQQLFYDRRYAESRVGA-----PDFVKVAEAYGIRGLR 526

Query: 554 CEREEDVVDVINQARAINDCPVVIDFIVGADAQVWPMVAAGTSNDEI 600
            +  E+  + I +  A +  PVV+DF+V  +  V+PMV  G   DE+
Sbjct: 527 AQTPEEAREAIREMLA-HPGPVVVDFVVPEEENVFPMVPPGAGTDEM 572


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: 1136
Number of extensions: 52
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: 578
Length adjustment: 37
Effective length of query: 581
Effective length of database: 541
Effective search space:   314321
Effective search space used:   314321
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_013074976.1 BTUS_RS04765 (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.32187.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-262  857.9   0.0   1.8e-262  857.7   0.0    1.0  1  lcl|NCBI__GCF_000092905.1:WP_013074976.1  BTUS_RS04765 acetolactate syntha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092905.1:WP_013074976.1  BTUS_RS04765 acetolactate synthase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  857.7   0.0  1.8e-262  1.8e-262       1     555 [.      24     574 ..      24     576 .. 0.99

  Alignments for each domain:
  == domain 1  score: 857.7 bits;  conditional E-value: 1.8e-262
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               ++gae+lve lk+egve++fGyPGGavlpiydaly s+++hil+rheq+a+haa+Gyar++G++Gvvla
  lcl|NCBI__GCF_000092905.1:WP_013074976.1  24 MTGAEMLVECLKREGVEIMFGYPGGAVLPIYDALYGSGIRHILTRHEQGAVHAAEGYARVTGRPGVVLA 92 
                                               79******************************************************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatnlvtgia+ay+ds+Plv++tGqvat+liGsd+fqe+di+Git+p+tkhs++v++a+d+p+++
  lcl|NCBI__GCF_000092905.1:WP_013074976.1  93 TSGPGATNLVTGIADAYMDSTPLVLFTGQVATDLIGSDSFQEADIIGITMPITKHSYQVRDAADIPRVV 161
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               +eaf+ia+tGrPGPvl+d+Pk+v++++  +e +e+v ++gy+pt +++++q+ k+ e+i+++++P+l+v
  lcl|NCBI__GCF_000092905.1:WP_013074976.1 162 REAFHIAATGRPGPVLIDVPKNVANQKAVFEWPERVFIRGYNPTYTPNPTQLSKVTEAIRESRRPLLYV 230
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgGv++++a eel+e+a+++ ipv++tl+GlGafp+ +pl++gmlGmhGt +an av e+dlliavGar
  lcl|NCBI__GCF_000092905.1:WP_013074976.1 231 GGGVVHSGAAEELREFAHKTGIPVVSTLMGLGAFPSADPLFVGMLGMHGTFAANRAVMECDLLIAVGAR 299
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekiee 345
                                               fddrvtg+l++f+p++k +hididPaeigknv+vd+p+vGd+k+vl+ +l ++  + +k   Wle+i+ 
  lcl|NCBI__GCF_000092905.1:WP_013074976.1 300 FDDRVTGKLERFSPHSKKVHIDIDPAEIGKNVAVDLPLVGDVKRVLSAMLPEVGPVGTKA--WLEQIRA 366
                                               ******************************************************999888..******* PP

                                 TIGR00118 346 wkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGf 414
                                               w ++ +l ++ e + +kPq+v++ l+  +++eai+tt+vGqhqmwaa fy++k+pr+++tsgGlGtmGf
  lcl|NCBI__GCF_000092905.1:WP_013074976.1 367 WDEQWPLGYKAEPGVLKPQQVLEMLWDATQGEAILTTEVGQHQMWAALFYRFKHPRQWVTSGGLGTMGF 435
                                               ********************************************************************* PP

                                 TIGR00118 415 GlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerys 483
                                               G+Paa+G+++akp etv++v+Gd+sfqmn+qel+t++e d+pvk+ i+nn +lGmv+qWq+lfy++ry+
  lcl|NCBI__GCF_000092905.1:WP_013074976.1 436 GFPAAMGVQLAKPGETVICVAGDASFQMNIQELQTVAENDLPVKVAIINNGFLGMVRQWQQLFYDRRYA 504
                                               ********************************************************************* PP

                                 TIGR00118 484 etklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGaglde 552
                                               e+ +++  pdfvk+aeayG++g+r ++pee+ e+++e+l++ +pv++d++v +ee+v+Pmv+pGag de
  lcl|NCBI__GCF_000092905.1:WP_013074976.1 505 ESRVGA--PDFVKVAEAYGIRGLRAQTPEEAREAIREMLAHPGPVVVDFVVPEEENVFPMVPPGAGTDE 571
                                               ****96..************************************************************* PP

                                 TIGR00118 553 lve 555
                                               +++
  lcl|NCBI__GCF_000092905.1:WP_013074976.1 572 MIG 574
                                               *96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (578 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: 11.20
//
[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