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.10462.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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.70
//
[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:

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:

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:

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:

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