Alignments for a candidate for ilvC in Methanococcus maripaludis C5

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Methanococcus maripaludis C5

Align ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate WP_011868682.1 MMARC5_RS04655 ketol-acid reductoisomerase

Query= BRENDA::A6UW80
         (329 letters)



>NCBI__GCF_000016125.1:WP_011868682.1
          Length = 330

 Score =  489 bits (1259), Expect = e-143
 Identities = 236/329 (71%), Positives = 277/329 (84%)

Query: 1   MKVYYEEDANYDAVKDKTIAVIGYGSQGMAQSCNMKDSGLNVIVGLRPNGASWEKAKADG 60
           MKV+Y+ D   DA+K+KTIAVIGYGSQG AQS NMKDSGLNV+VGLR NGASWE AKADG
Sbjct: 1   MKVFYDSDFKLDALKEKTIAVIGYGSQGRAQSLNMKDSGLNVVVGLRKNGASWENAKADG 60

Query: 61  HTVMSVEEAAEKADIIHILIPDEVQKDVYNNQIKQHLTEGKTLSFSHGYNVHFKYIDPIK 120
           H VM++EEAAEKADIIHILIPDE+Q +VY +QIK +L EGKTLSFSHG+N+H+ +I P K
Sbjct: 61  HNVMTIEEAAEKADIIHILIPDELQAEVYESQIKPYLKEGKTLSFSHGFNIHYGFIVPPK 120

Query: 121 GVNVIMVAPKSPGAMVRRTYTEGFGVPGLVCVERDETGDALDIALGMAKAEGLTKAGVIK 180
           GVNV++VAPKSPG MVRRTY EGFGVPGL+C+E D T +A DI   MAK  GL++AGVI+
Sbjct: 121 GVNVVLVAPKSPGKMVRRTYEEGFGVPGLICIEIDATNNAFDIVSAMAKGIGLSRAGVIQ 180

Query: 181 TTFKEETETDLFGEQAVLCGGVTELIKAGFDTLVEAGYSPEMAYFETCNELKLIVDLIYQ 240
           TTFKEETETDLFGEQAVLCGGVTELIKAGF+TLVEAGY+PEMAYFETC+ELKLIVDLIYQ
Sbjct: 181 TTFKEETETDLFGEQAVLCGGVTELIKAGFETLVEAGYAPEMAYFETCHELKLIVDLIYQ 240

Query: 241 KGLAGMWNDVSNTAEYGGFVTRERVINEESRKAMREILKEIQNGKFARDWALENVSGIPH 300
           KG   MWNDVSNTAEYGG   R R++  +S+ AM+EILKEIQ+G+F +++ LE      H
Sbjct: 241 KGFKNMWNDVSNTAEYGGLTRRSRIVTADSKAAMKEILKEIQDGRFTKEFVLEKQVNHAH 300

Query: 301 LNAMRRLEDESLLETTGKKLRKMCGLQKD 329
           L AMRR+E +  +E  G KLRKMCGL+K+
Sbjct: 301 LKAMRRIEGDLQIEEVGAKLRKMCGLEKE 329


Lambda     K      H
   0.316    0.134    0.386 

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: 397
Number of extensions: 9
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: 329
Length of database: 330
Length adjustment: 28
Effective length of query: 301
Effective length of database: 302
Effective search space:    90902
Effective search space used:    90902
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_011868682.1 MMARC5_RS04655 (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.5006.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-150  486.2   2.0     2e-150  486.0   2.0    1.0  1  lcl|NCBI__GCF_000016125.1:WP_011868682.1  MMARC5_RS04655 ketol-acid reduct


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016125.1:WP_011868682.1  MMARC5_RS04655 ketol-acid reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  486.0   2.0    2e-150    2e-150       1     314 []      14     328 ..      14     328 .. 0.99

  Alignments for each domain:
  == domain 1  score: 486.0 bits;  conditional E-value: 2e-150
                                 TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 
                                               lk+k++a+iGyGsqG+aq+ln++dsglnv+vglrk++asw++A+ dG++v+t+eea++kad+i+iL+pD
  lcl|NCBI__GCF_000016125.1:WP_011868682.1  14 LKEKTIAVIGYGSQGRAQSLNMKDSGLNVVVGLRKNGASWENAKADGHNVMTIEEAAEKADIIHILIPD 82 
                                               799****************************************************************** PP

                                 TIGR00465  70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138
                                               e+q evye +ikp+lkegk+l+fsHGfni++  iv+pk+v+vvlvAPK+pG++vR++y+eg+Gvp+li 
  lcl|NCBI__GCF_000016125.1:WP_011868682.1  83 ELQAEVYESQIKPYLKEGKTLSFSHGFNIHYGFIVPPKGVNVVLVAPKSPGKMVRRTYEEGFGVPGLIC 151
                                               ********************************************************************* PP

                                 TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207
                                               +e d+t +a +i  a+Ak+iG +ragv++ttFkeE+e+DLfGEqavLcGg+++lika+f+tLveaGy+p
  lcl|NCBI__GCF_000016125.1:WP_011868682.1 152 IEIDATNNAFDIVSAMAKGIGLSRAGVIQTTFKEETETDLFGEQAVLCGGVTELIKAGFETLVEAGYAP 220
                                               ********************************************************************* PP

                                 TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275
                                               e+Ayfe++helklivdl+++kG+++m++ vsntA++g+l++r +i+++  k++m++ilkeiq+G+f+ke
  lcl|NCBI__GCF_000016125.1:WP_011868682.1 221 EMAYFETCHELKLIVDLIYQKGFKNMWNDVSNTAEYGGLTRRsRIVTADSKAAMKEILKEIQDGRFTKE 289
                                               *****************************************99************************** PP

                                 TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvkaek 314
                                               ++lek++++++++++r+ e + +ie+vG +lr+++ +ek
  lcl|NCBI__GCF_000016125.1:WP_011868682.1 290 FVLEKQVNHAHLKAMRRIEGDLQIEEVGAKLRKMCGLEK 328
                                               ***********************************9875 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 9.72
//
[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