Alignments for a candidate for ilvC in Nocardiopsis lucentensis DSM 44048

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Nocardiopsis lucentensis DSM 44048

Align ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate WP_017598159.1 D471_RS0108140 ketol-acid reductoisomerase

Query= BRENDA::A0A0K2AZ61
         (332 letters)



>NCBI__GCF_000341125.1:WP_017598159.1
          Length = 327

 Score =  474 bits (1220), Expect = e-138
 Identities = 230/325 (70%), Positives = 269/325 (82%)

Query: 4   LFYDADADLSIIQGRKVAVIGYGSQGHAHALSLRDSGVDVRVGLHEGSKSKAKAEEQGLR 63
           ++YD  ADL +IQ +KVAVIGYGSQGHAHALSLRDSGVDVR+GL EGSKS+AKAEE+GLR
Sbjct: 1   MYYDDAADLELIQSKKVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSKSRAKAEEEGLR 60

Query: 64  VVSPSEAAAEADVIMILVPDPIQAQVYEEHIKDNLKDGDALFFGHGLNIRFGFIKPPAGV 123
           V++P+EAA EADVIMILVPD I   +Y   I  NL+ G+ALFFGHG +IR+G I PP GV
Sbjct: 61  VLTPAEAAREADVIMILVPDHIHRDLYANEIAPNLEAGNALFFGHGFSIRYGLITPPEGV 120

Query: 124 DVCMVAPKGPGHLVRRQYEEGRGVPCIAAVEQDASGNAFALALSYAKGIGGTRAGVIKTT 183
           DV MVAPKGPGHLVRRQYE GRGVPC+ AVE+DASG A+ LALS+AKGIGGT+AGVIKTT
Sbjct: 121 DVAMVAPKGPGHLVRRQYEAGRGVPCLVAVEKDASGQAWDLALSWAKGIGGTKAGVIKTT 180

Query: 184 FTEETETDLFGEQAVLCGGTAALVKAGFETLTEAGYQPEIAYFECLHELKLIVDLMYEGG 243
           FTEETETDLFGEQAVLCGGT  LVKAGF TL EAGYQPEIAYFECLHELKLIVDLMYEGG
Sbjct: 181 FTEETETDLFGEQAVLCGGTEELVKAGFATLVEAGYQPEIAYFECLHELKLIVDLMYEGG 240

Query: 244 LEKMRWSISETAEWGDYVTGPRIITDATKAEMKKVLAEIQDGTFAKNWMDEYHGGLKKYN 303
           + KM WS+S+ AE+G Y  GPR+IT+ T+ EM+K+L EIQDG++AK  MDE+  G   + 
Sbjct: 241 ISKMNWSVSDNAEYGGYTRGPRVITEQTREEMRKILREIQDGSYAKELMDEFDAGQPTFT 300

Query: 304 EYKQQDSEHLLETTGKQLRKLMSWV 328
           + ++ +    +E  G QLR LMSW+
Sbjct: 301 KRREAEQNEPIEKVGAQLRPLMSWL 325


Lambda     K      H
   0.316    0.135    0.395 

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: 426
Number of extensions: 13
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: 332
Length of database: 327
Length adjustment: 28
Effective length of query: 304
Effective length of database: 299
Effective search space:    90896
Effective search space used:    90896
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_017598159.1 D471_RS0108140 (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.30299.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-135  436.8   0.0   2.2e-135  436.6   0.0    1.0  1  lcl|NCBI__GCF_000341125.1:WP_017598159.1  D471_RS0108140 ketol-acid reduct


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000341125.1:WP_017598159.1  D471_RS0108140 ketol-acid reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  436.6   0.0  2.2e-135  2.2e-135       1     313 [.      12     325 ..      12     326 .. 0.99

  Alignments for each domain:
  == domain 1  score: 436.6 bits;  conditional E-value: 2.2e-135
                                 TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 
                                               +++kkva+iGyGsqG+a+al lrdsg++v++gl ++++s +kAee+G++vlt +ea+++ad+imiL+pD
  lcl|NCBI__GCF_000341125.1:WP_017598159.1  12 IQSKKVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSKSRAKAEEEGLRVLTPAEAAREADVIMILVPD 80 
                                               689****************************************************************** PP

                                 TIGR00465  70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138
                                               +++++ y +ei+p+l++g+al f HGf+i +  i++p++vdv++vAPKgpG+lvR++y+ grGvp l+A
  lcl|NCBI__GCF_000341125.1:WP_017598159.1  81 HIHRDLYANEIAPNLEAGNALFFGHGFSIRYGLITPPEGVDVAMVAPKGPGHLVRRQYEAGRGVPCLVA 149
                                               ********************************************************************* PP

                                 TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207
                                               ve+d++g+a + Al++Ak+iGg++agv++ttF eE+e+DLfGEqavLcGg e+l+ka+f tLveaGyqp
  lcl|NCBI__GCF_000341125.1:WP_017598159.1 150 VEKDASGQAWDLALSWAKGIGGTKAGVIKTTFTEETETDLFGEQAVLCGGTEELVKAGFATLVEAGYQP 218
                                               ********************************************************************* PP

                                 TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275
                                               e+Ayfe++helklivdl++e+G+++m  +vs+ A++g+++++ ++++e++++em+kil eiq+G++ake
  lcl|NCBI__GCF_000341125.1:WP_017598159.1 219 EIAYFECLHELKLIVDLMYEGGISKMNWSVSDNAEYGGYTRGpRVITEQTREEMRKILREIQDGSYAKE 287
                                               ********************************************************************* PP

                                 TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvkae 313
                                                + e+ ag+p+f++ r++e+++ iekvG +lr l+++ 
  lcl|NCBI__GCF_000341125.1:WP_017598159.1 288 LMDEFDAGQPTFTKRREAEQNEPIEKVGAQLRPLMSWL 325
                                               **********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (327 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: 6.94
//
[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