Alignments for a candidate for ilvC in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Desulfovibrio vulgaris Hildenborough

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 206820 DVU1378 ketol-acid reductoisomerase

Query= SwissProt::K4LVZ1
         (332 letters)



>MicrobesOnline__882:206820
          Length = 331

 Score =  471 bits (1211), Expect = e-137
 Identities = 225/331 (67%), Positives = 273/331 (82%)

Query: 1   MKIYYDQDADLQYLDGKTVAVIGYGSQGHAQSQNLRDSGVKVVVADIPSSENWKKAEEAQ 60
           MK+YY++DA+L+ L GKTVA+IGYGSQGHA +QNLRDSG+ V+V   P   N+  A+E  
Sbjct: 1   MKVYYEKDANLEALKGKTVAIIGYGSQGHAHAQNLRDSGISVIVGQRPGGANYALAKEHG 60

Query: 61  FQPLTADEAAREADIIQILVPDEKQAALYRESIAPNLRPGKALVFSHGFNIHFKQIVPPP 120
           F+P++A EAA +AD+I IL+PD+ QAA+Y   I PNL+ G AL+F+HGFNIHF QI PP 
Sbjct: 61  FEPVSAAEAAAKADLIMILLPDQVQAAVYEAEIKPNLKAGDALLFAHGFNIHFGQIEPPK 120

Query: 121 DVDVFMVAPKGPGHLVRRMYEEGAGVPSLVAVEQDYSGQALNLALAYAKGIGATRAGVIQ 180
           DVDVFM+APKGPGHLVRR Y EG GVP LVAV QD +G+A+  ALAYAKG+G +R+GVI+
Sbjct: 121 DVDVFMIAPKGPGHLVRRTYTEGGGVPCLVAVHQDATGKAMEKALAYAKGVGGSRSGVIE 180

Query: 181 TTFKEETETDLFGEQAVLCGGITELIRAGFDTLVDAGYQPEIAYFECLHEMKLIVDLIYE 240
           TTF+EETETDLFGEQAVLCGG++ LI+AGF+TLV+AGYQPEIAYFECLHE+KLIVDLIYE
Sbjct: 181 TTFREETETDLFGEQAVLCGGLSSLIKAGFETLVEAGYQPEIAYFECLHEVKLIVDLIYE 240

Query: 241 GGISTMRYSISDTAEYGDLTRGKRIITEATREEMKKILKEIQDGVFAREWLLENQVGRPV 300
           GG+  MRYSISDTAEYGD   GKRI+TE T++EMKK+L++IQDG FAR ++LE + G P 
Sbjct: 241 GGLERMRYSISDTAEYGDYVTGKRIVTEETKKEMKKVLRDIQDGTFARNFILEAKAGYPG 300

Query: 301 YNALRRKEQNHLIETVGARLRGMMPWLKKKV 331
           + A RR E  H IE VG  LRGMMPWLKKKV
Sbjct: 301 FKATRRLEAEHQIEKVGGELRGMMPWLKKKV 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: 385
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: 331
Length adjustment: 28
Effective length of query: 304
Effective length of database: 303
Effective search space:    92112
Effective search space used:    92112
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 206820 DVU1378 (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.15221.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.4e-146  473.3   0.3   1.7e-146  473.1   0.3    1.0  1  lcl|MicrobesOnline__882:206820  DVU1378 ketol-acid reductoisomer


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:206820  DVU1378 ketol-acid reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  473.1   0.3  1.7e-146  1.7e-146       1     314 []      14     328 ..      14     328 .. 0.99

  Alignments for each domain:
  == domain 1  score: 473.1 bits;  conditional E-value: 1.7e-146
                       TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqkevyeae 79 
                                     lkgk+vaiiGyGsqG+a+a nlrdsg+ vivg r+++a ++ A+e Gf+ ++ +ea++kadlimiLlpD+vq +vyeae
  lcl|MicrobesOnline__882:206820  14 LKGKTVAIIGYGSQGHAHAQNLRDSGISVIVGQRPGGANYALAKEHGFEPVSAAEAAAKADLIMILLPDQVQAAVYEAE 92 
                                     79***************************************************************************** PP

                       TIGR00465  80 ikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtgeakeiAlayAkai 158
                                     ikp+lk+g+allf+HGfni+f qi++pkdvdv+++APKgpG+lvR++y eg Gvp l+Av+qd+tg+a+e+AlayAk++
  lcl|MicrobesOnline__882:206820  93 IKPNLKAGDALLFAHGFNIHFGQIEPPKDVDVFMIAPKGPGHLVRRTYTEGGGVPCLVAVHQDATGKAMEKALAYAKGV 171
                                     ******************************************************************************* PP

                       TIGR00465 159 GgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelklivdllkekGlelmrdav 237
                                     Gg+r gv+ettF+eE+e+DLfGEqavLcGgl+ lika+f+tLveaGyqpe+Ayfe++he+klivdl++e+Gle mr ++
  lcl|MicrobesOnline__882:206820 172 GGSRSGVIETTFREETETDLFGEQAVLCGGLSSLIKAGFETLVEAGYQPEIAYFECLHEVKLIVDLIYEGGLERMRYSI 250
                                     ******************************************************************************* PP

                       TIGR00465 238 sntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeearkkekeqeiekvGkelralvkaek 314
                                     s+tA++g++ ++ +i++ee+kkem+k+l +iq+G+fa++++le +ag+p f+++r+ e e++iekvG elr ++++ k
  lcl|MicrobesOnline__882:206820 251 SDTAEYGDYVTGkRIVTEETKKEMKKVLRDIQDGTFARNFILEAKAGYPGFKATRRLEAEHQIEKVGGELRGMMPWLK 328
                                     *********9999*************************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (331 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: 8.46
//
[ok]

This GapMind analysis is from Apr 09 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