Alignments for a candidate for ilvC in Thioalkalivibrio thiocyanodenitrificans ARhD 1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Thioalkalivibrio thiocyanodenitrificans ARhD 1

Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate WP_018232000.1 THITHI_RS0105105 ketol-acid reductoisomerase

Query= metacyc::MONOMER-18814
         (338 letters)



>NCBI__GCF_000378965.1:WP_018232000.1
          Length = 338

 Score =  489 bits (1259), Expect = e-143
 Identities = 239/338 (70%), Positives = 284/338 (84%)

Query: 1   MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGVNVTVGLRKSGASWNKAANAG 60
           M+V+YDKDADLS+I+G  V I+GYGSQGHAHA NLKDSGV+VTV LR   AS  KA  AG
Sbjct: 1   MQVYYDKDADLSIIQGMKVAIVGYGSQGHAHANNLKDSGVDVTVALRAGSASARKAEGAG 60

Query: 61  LQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPRA 120
           L+V+ + +AVKGAD+VMIL PDE  A +Y+++V  N+K+G  LAFAHGFN+H+  + PR+
Sbjct: 61  LKVQGIEDAVKGADLVMILAPDEHQAALYQDQVGPNLKQGGVLAFAHGFNIHFEQIEPRS 120

Query: 121 DLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGIIE 180
           DLDVIM+APK PGH VR+TYTQGGGVP LIAV+Q+ SG ARDIALSYA+ANGGGRAGIIE
Sbjct: 121 DLDVIMVAPKGPGHLVRSTYTQGGGVPSLIAVYQDASGRARDIALSYASANGGGRAGIIE 180

Query: 181 TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240
           T+F++ETETDLFGEQAVLCGG   L++AGFETLVEAGY PEMAYFECLHELKLIVDL+YE
Sbjct: 181 TSFKDETETDLFGEQAVLCGGATALVQAGFETLVEAGYPPEMAYFECLHELKLIVDLMYE 240

Query: 241 GGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAPT 300
           GGIA+M YSISN AEYG+   GPRVVTE+TK  MK+ LT+IQTG +A+ F+LENKAGA T
Sbjct: 241 GGIADMRYSISNTAEYGDITRGPRVVTEQTKAEMKKILTEIQTGRFAREFILENKAGAAT 300

Query: 301 LISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338
           L + RR+  EH IE VG++LR MMPWI  NKMVD+SKN
Sbjct: 301 LKASRRIAREHPIEVVGSRLRDMMPWIKANKMVDKSKN 338


Lambda     K      H
   0.316    0.133    0.379 

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: 459
Number of extensions: 12
Number of successful extensions: 1
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: 338
Length of database: 338
Length adjustment: 28
Effective length of query: 310
Effective length of database: 310
Effective search space:    96100
Effective search space used:    96100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_018232000.1 THITHI_RS0105105 (ketol-acid reductoisomerase)
to HMM TIGR00465 (ilvC: ketol-acid reductoisomerase (EC 1.1.1.86))

# 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/TIGR00465.hmm
# target sequence database:        /tmp/gapView.13064.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00465  [M=314]
Accession:   TIGR00465
Description: ilvC: ketol-acid reductoisomerase
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-140  453.6   0.4   1.7e-140  453.4   0.4    1.0  1  lcl|NCBI__GCF_000378965.1:WP_018232000.1  THITHI_RS0105105 ketol-acid redu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000378965.1:WP_018232000.1  THITHI_RS0105105 ketol-acid reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  453.4   0.4  1.7e-140  1.7e-140       1     313 [.      14     327 ..      14     328 .. 0.99

  Alignments for each domain:
  == domain 1  score: 453.4 bits;  conditional E-value: 1.7e-140
                                 TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 
                                               ++g kvai+GyGsqG+a+a nl+dsg++v+v+lr ++as +kAe  G+kv  +e+a+k adl+miL pD
  lcl|NCBI__GCF_000378965.1:WP_018232000.1  14 IQGMKVAIVGYGSQGHAHANNLKDSGVDVTVALRAGSASARKAEGAGLKVQGIEDAVKGADLVMILAPD 82 
                                               6899***************************************************************** PP

                                 TIGR00465  70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138
                                               e q + y+ ++ p+lk+g +l f+HGfni+f+qi+++ d+dv++vAPKgpG+lvR++y +g GvpsliA
  lcl|NCBI__GCF_000378965.1:WP_018232000.1  83 EHQAALYQDQVGPNLKQGGVLAFAHGFNIHFEQIEPRSDLDVIMVAPKGPGHLVRSTYTQGGGVPSLIA 151
                                               ********************************************************************* PP

                                 TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207
                                               v+qd++g a++iAl+yA a Gg+rag++et+Fk+E+e+DLfGEqavLcGg +al++a+f+tLveaGy p
  lcl|NCBI__GCF_000378965.1:WP_018232000.1 152 VYQDASGRARDIALSYASANGGGRAGIIETSFKDETETDLFGEQAVLCGGATALVQAGFETLVEAGYPP 220
                                               ********************************************************************* PP

                                 TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275
                                               e+Ayfe++helklivdl++e+G++ mr ++sntA++g+++++ ++++e++k+em+kil eiq+G+fa+e
  lcl|NCBI__GCF_000378965.1:WP_018232000.1 221 EMAYFECLHELKLIVDLMYEGGIADMRYSISNTAEYGDITRGpRVVTEQTKAEMKKILTEIQTGRFARE 289
                                               ********************************************************************* PP

                                 TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvkae 313
                                               ++le++ag++++++ r+  +e+ ie vG++lr+++++ 
  lcl|NCBI__GCF_000378965.1:WP_018232000.1 290 FILENKAGAATLKASRRIAREHPIEVVGSRLRDMMPWI 327
                                               ***********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (338 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.70
//
[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