Alignments for a candidate for ilvC in Steroidobacter denitrificans DSM 18526

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Steroidobacter denitrificans DSM 18526

Align Ketol-acid reductoisomerase (NAD(P)(+)); KARI; Acetohydroxy-acid isomeroreductase; AHIR; Alpha-keto-beta-hydroxylacyl reductoisomerase; Ketol-acid reductoisomerase type 1; Ketol-acid reductoisomerase type I; EC 1.1.1.383 (characterized)
to candidate WP_066920219.1 ACG33_RS08090 ketol-acid reductoisomerase

Query= SwissProt::O28294
         (332 letters)



>NCBI__GCF_001579945.1:WP_066920219.1
          Length = 330

 Score =  377 bits (969), Expect = e-109
 Identities = 188/329 (57%), Positives = 241/329 (73%), Gaps = 2/329 (0%)

Query: 3   KIYRDADADLKYLDGKTVCIIGYGSQGHAHALNLKDSGVNVVVGLPEWDKATWERAEKDG 62
           +IY   D   K L G  + I+GYGSQG AHALNLKDSG +VVVG+ + +  +W+ A+KDG
Sbjct: 2   QIYSQKDVKKKALKGARIAILGYGSQGRAHALNLKDSGFDVVVGVRK-NGDSWKNAKKDG 60

Query: 63  MVVKKLSEAADGADVIAMLIPDMVQPAVYREHIQDKLKEGAMLMFAHGFNIHYNQIVPPE 122
           + V + ++A  GA +IA L PD+ Q  VY E I D + +GA ++FAHGFN+H+ QI P +
Sbjct: 61  LPVAEPADAVKGAALIAFLTPDLTQKDVYAEVI-DNIAKGATILFAHGFNVHFKQIKPRQ 119

Query: 123 YVDVAMVAPKGPGPLVRRMYVEGKGVPSLVAVEQNYTGKALEVALAYAKGIGATRAGVIE 182
            +DV ++APKGPG LVRR Y +G+GVP L+AV QN T KA + ALAYA GIG TR GV+ 
Sbjct: 120 DLDVVLIAPKGPGGLVRRQYQQGRGVPCLMAVYQNATRKAKDNALAYADGIGGTRGGVLT 179

Query: 183 TTFKEETETDLFGEQVDLCGGVAEMIKMSFETLVEAGYQPEIAYFEVLHELKLIVDLIYE 242
           TTF EETETDLFGEQ  LCGG  E++   FETLVEAGYQPE+AY+E LHELKLIVDL++E
Sbjct: 180 TTFAEETETDLFGEQAVLCGGATELVVKGFETLVEAGYQPEVAYYECLHELKLIVDLLHE 239

Query: 243 GGIYNMWSAVSETAKYGGMTRGKRIFTEQTREEMRKILKEIQTGEFAREWILENMAGRPV 302
           GG+  M   +SETAKYG +TRG RI    T+ EM+K+LKEIQ G+FAR+WI EN  GR  
Sbjct: 240 GGLAKMHQFISETAKYGDLTRGPRIVNAATKREMKKVLKEIQDGKFARQWIAENKRGRKR 299

Query: 303 YNKLLQMEREHPIEKIGKELRAMMPWLKK 331
           Y +L+  + +H IEK+G +LR  MPWL++
Sbjct: 300 YKQLMNKDLKHKIEKVGVKLRRRMPWLQE 328


Lambda     K      H
   0.318    0.136    0.399 

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: 359
Number of extensions: 21
Number of successful extensions: 3
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: 332
Length of database: 330
Length adjustment: 28
Effective length of query: 304
Effective length of database: 302
Effective search space:    91808
Effective search space used:    91808
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_066920219.1 ACG33_RS08090 (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.362375.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.8e-133  428.9   0.2   5.5e-133  428.7   0.2    1.0  1  NCBI__GCF_001579945.1:WP_066920219.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001579945.1:WP_066920219.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  428.7   0.2  5.5e-133  5.5e-133       1     313 [.      14     326 ..      14     327 .. 0.99

  Alignments for each domain:
  == domain 1  score: 428.7 bits;  conditional E-value: 5.5e-133
                             TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqk 73 
                                           lkg ++ai+GyGsqG+a+alnl+dsg +v+vg+rk++ swk+A++dG+ v + ++a+k a li+ L+pD +qk
  NCBI__GCF_001579945.1:WP_066920219.1  14 LKGARIAILGYGSQGRAHALNLKDSGFDVVVGVRKNGDSWKNAKKDGLPVAEPADAVKGAALIAFLTPDLTQK 86 
                                           7899******************************************************************999 PP

                             TIGR00465  74 evyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtge 146
                                           +vy + + +++ +g+++lf+HGfn++fkqi++++d+dvvl+APKgpG lvR++y++grGvp l+Av+q++t +
  NCBI__GCF_001579945.1:WP_066920219.1  87 DVYAE-VIDNIAKGATILFAHGFNVHFKQIKPRQDLDVVLIAPKGPGGLVRRQYQQGRGVPCLMAVYQNATRK 158
                                           99977.99***************************************************************** PP

                             TIGR00465 147 akeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelk 219
                                           ak+ AlayA +iGg+r gvl ttF eE+e+DLfGEqavLcGg ++l+  +f+tLveaGyqpe+Ay e++helk
  NCBI__GCF_001579945.1:WP_066920219.1 159 AKDNALAYADGIGGTRGGVLTTTFAEETETDLFGEQAVLCGGATELVVKGFETLVEAGYQPEVAYYECLHELK 231
                                           ************************************************************************* PP

                             TIGR00465 220 livdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeear 291
                                           livdll+e+Gl++m + +s+tAk+g+l+++ +i+++++k+em+k+lkeiq+G+fa++w+ e++ g+ ++++  
  NCBI__GCF_001579945.1:WP_066920219.1 232 LIVDLLHEGGLAKMHQFISETAKYGDLTRGpRIVNAATKREMKKVLKEIQDGKFARQWIAENKRGRKRYKQLM 304
                                           ************************************************************************* PP

                             TIGR00465 292 kkekeqeiekvGkelralvkae 313
                                           +k+ +++iekvG++lr+ +++ 
  NCBI__GCF_001579945.1:WP_066920219.1 305 NKDLKHKIEKVGVKLRRRMPWL 326
                                           *****************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (330 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 16.94
//
[ok]

This GapMind analysis is from Jul 25 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:

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