Alignments for a candidate for ilvC in Dehalococcoides mccartyi 195

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Dehalococcoides mccartyi 195

Align Ketol-acid reductoisomerase (NAD(+)); KARI; Acetohydroxy-acid isomeroreductase; AHIR; Alpha-keto-beta-hydroxylacyl reductoisomerase; Ketol-acid reductoisomerase type 1; Ketol-acid reductoisomerase type I; EC 1.1.1.382 (characterized)
to candidate WP_010936559.1 DET_RS04335 ketol-acid reductoisomerase

Query= SwissProt::K4LVZ1
         (332 letters)



>NCBI__GCF_000011905.1:WP_010936559.1
          Length = 332

 Score =  447 bits (1151), Expect = e-130
 Identities = 212/328 (64%), Positives = 263/328 (80%)

Query: 3   IYYDQDADLQYLDGKTVAVIGYGSQGHAQSQNLRDSGVKVVVADIPSSENWKKAEEAQFQ 62
           IYYD+D DL  ++ K + ++GYG+QGHA +QNLRDSG+KV+VA +     WKKA    F+
Sbjct: 4   IYYDKDCDLSLIEKKIIGIVGYGAQGHAHAQNLRDSGLKVIVACVEGGRGWKKATADGFE 63

Query: 63  PLTADEAAREADIIQILVPDEKQAALYRESIAPNLRPGKALVFSHGFNIHFKQIVPPPDV 122
            +   E A++ADII +L PD  QA +Y++S+   L PGK L+F+HGFNIH+ QIVPP  V
Sbjct: 64  VMCVAEMAKKADIIMMLAPDTSQAKIYKDSVEQGLTPGKMLMFAHGFNIHYGQIVPPSFV 123

Query: 123 DVFMVAPKGPGHLVRRMYEEGAGVPSLVAVEQDYSGQALNLALAYAKGIGATRAGVIQTT 182
           DV M+APK PG+++R+++ EGAG PSL+AVEQD SG+A  +ALAYAKGIG+ RAGV++TT
Sbjct: 124 DVTMIAPKCPGYMLRQVFTEGAGAPSLIAVEQDASGKAKEIALAYAKGIGSNRAGVLETT 183

Query: 183 FKEETETDLFGEQAVLCGGITELIRAGFDTLVDAGYQPEIAYFECLHEMKLIVDLIYEGG 242
           F EETETDLFGEQAVLCGG T L++AGF+TLV+AGYQPE+AYFECLHE+KLIVDL+Y+GG
Sbjct: 184 FAEETETDLFGEQAVLCGGTTSLVKAGFETLVEAGYQPEVAYFECLHELKLIVDLMYQGG 243

Query: 243 ISTMRYSISDTAEYGDLTRGKRIITEATREEMKKILKEIQDGVFAREWLLENQVGRPVYN 302
           I+ MR SISDTA+YGD TRG R+I E T E M +IL EIQDG FA+EW+LENQ GRPVYN
Sbjct: 244 IAYMRDSISDTAKYGDFTRGPRVINEETYETMGEILGEIQDGSFAKEWILENQAGRPVYN 303

Query: 303 ALRRKEQNHLIETVGARLRGMMPWLKKK 330
           +LRR E  HLIE VGA LR MM WLKKK
Sbjct: 304 SLRRMESEHLIEEVGAELRSMMSWLKKK 331


Lambda     K      H
   0.318    0.136    0.393 

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: 364
Number of extensions: 7
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: 332
Length adjustment: 28
Effective length of query: 304
Effective length of database: 304
Effective search space:    92416
Effective search space used:    92416
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_010936559.1 DET_RS04335 (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.9062.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.2e-141  456.3   0.6   2.7e-141  456.0   0.6    1.0  1  lcl|NCBI__GCF_000011905.1:WP_010936559.1  DET_RS04335 ketol-acid reductois


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000011905.1:WP_010936559.1  DET_RS04335 ketol-acid reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.0   0.6  2.7e-141  2.7e-141       2     314 .]      16     329 ..      15     329 .. 0.99

  Alignments for each domain:
  == domain 1  score: 456.0 bits;  conditional E-value: 2.7e-141
                                 TIGR00465   2 kgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDe 70 
                                               ++k ++i+GyG+qG+a+a nlrdsgl+viv+  +++  wkkA+ dGf+v+ v+e++kkad+im+L pD+
  lcl|NCBI__GCF_000011905.1:WP_010936559.1  16 EKKIIGIVGYGAQGHAHAQNLRDSGLKVIVACVEGGRGWKKATADGFEVMCVAEMAKKADIIMMLAPDT 84 
                                               67889**************************************************************** PP

                                 TIGR00465  71 vqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAv 139
                                                q + y+ ++++ l+ gk+l+f+HGfni++ qiv+p  vdv+++APK+pG ++R+ + eg+G psliAv
  lcl|NCBI__GCF_000011905.1:WP_010936559.1  85 SQAKIYKDSVEQGLTPGKMLMFAHGFNIHYGQIVPPSFVDVTMIAPKCPGYMLRQVFTEGAGAPSLIAV 153
                                               ********************************************************************* PP

                                 TIGR00465 140 eqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpe 208
                                               eqd++g+akeiAlayAk+iG++ragvlettF eE+e+DLfGEqavLcGg + l+ka+f+tLveaGyqpe
  lcl|NCBI__GCF_000011905.1:WP_010936559.1 154 EQDASGKAKEIALAYAKGIGSNRAGVLETTFAEETETDLFGEQAVLCGGTTSLVKAGFETLVEAGYQPE 222
                                               ********************************************************************* PP

                                 TIGR00465 209 lAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakew 276
                                               +Ayfe++helklivdl++++G+++mrd++s+tAk+g+++++ ++++ee+ ++m +il eiq+G+fakew
  lcl|NCBI__GCF_000011905.1:WP_010936559.1 223 VAYFECLHELKLIVDLMYQGGIAYMRDSISDTAKYGDFTRGpRVINEETYETMGEILGEIQDGSFAKEW 291
                                               ********************************************************************* PP

                                 TIGR00465 277 alekeagkpafeearkkekeqeiekvGkelralvkaek 314
                                               +le++ag+p +++ r++e+e+ ie+vG elr ++++ k
  lcl|NCBI__GCF_000011905.1:WP_010936559.1 292 ILENQAGRPVYNSLRRMESEHLIEEVGAELRSMMSWLK 329
                                               **********************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (332 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: 11.63
//
[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