Alignments for a candidate for ilvC in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Desulfovibrio vulgaris Miyazaki F

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 8499378 DvMF_0155 ketol-acid reductoisomerase (RefSeq)

Query= SwissProt::K4LVZ1
         (332 letters)



>FitnessBrowser__Miya:8499378
          Length = 330

 Score =  463 bits (1192), Expect = e-135
 Identities = 222/330 (67%), Positives = 269/330 (81%)

Query: 1   MKIYYDQDADLQYLDGKTVAVIGYGSQGHAQSQNLRDSGVKVVVADIPSSENWKKAEEAQ 60
           MK+YY+QDA L+ L  KTVA+IGYGSQGHA +QNLRDSG+ VVV   P   N++ A+E  
Sbjct: 1   MKVYYEQDATLEVLKDKTVAIIGYGSQGHAHAQNLRDSGINVVVGQRPGGANYELAKEHG 60

Query: 61  FQPLTADEAAREADIIQILVPDEKQAALYRESIAPNLRPGKALVFSHGFNIHFKQIVPPP 120
           F PL   EAA +AD+I IL+PD+ QAA+Y   I PNL+PG AL+F+HGFNIHF QI PP 
Sbjct: 61  FAPLPVAEAAAKADLIMILLPDQVQAAIYEAEIKPNLKPGDALLFAHGFNIHFGQIEPPK 120

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

Query: 181 TTFKEETETDLFGEQAVLCGGITELIRAGFDTLVDAGYQPEIAYFECLHEMKLIVDLIYE 240
           TTFKEETETDLFGEQAVLCGG++ LI+AGF+TLV+AGYQPEIAYFECLHE+KLIVDLIYE
Sbjct: 181 TTFKEETETDLFGEQAVLCGGLSSLIKAGFETLVEAGYQPEIAYFECLHEVKLIVDLIYE 240

Query: 241 GGISTMRYSISDTAEYGDLTRGKRIITEATREEMKKILKEIQDGVFAREWLLENQVGRPV 300
           GG++ MR+SISDTAEYGD   G+RI+ E T++EMKK+L+EIQ+G FAR ++LE + G P 
Sbjct: 241 GGLAKMRHSISDTAEYGDYVTGRRIVNEETKKEMKKVLQEIQEGTFARNFILEAKAGYPG 300

Query: 301 YNALRRKEQNHLIETVGARLRGMMPWLKKK 330
           + A RR E +H IE VG +LRGMMPWL KK
Sbjct: 301 FKATRRIEADHQIEQVGGKLRGMMPWLHKK 330


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: 378
Number of extensions: 12
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: 330
Length adjustment: 28
Effective length of query: 304
Effective length of database: 302
Effective search space:    91808
Effective search space used:    91808
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 8499378 DvMF_0155 (ketol-acid reductoisomerase (RefSeq))
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.26450.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.7e-146  471.2   0.2   7.9e-146  470.9   0.2    1.0  1  lcl|FitnessBrowser__Miya:8499378  DvMF_0155 ketol-acid reductoisom


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8499378  DvMF_0155 ketol-acid reductoisomerase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  470.9   0.2  7.9e-146  7.9e-146       1     312 [.      14     326 ..      14     328 .. 0.99

  Alignments for each domain:
  == domain 1  score: 470.9 bits;  conditional E-value: 7.9e-146
                         TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqkevye 77 
                                       lk+k+vaiiGyGsqG+a+a nlrdsg+nv+vg r+++a ++ A+e Gf  l v+ea++kadlimiLlpD+vq + ye
  lcl|FitnessBrowser__Miya:8499378  14 LKDKTVAIIGYGSQGHAHAQNLRDSGINVVVGQRPGGANYELAKEHGFAPLPVAEAAAKADLIMILLPDQVQAAIYE 90 
                                       79*************************************************************************** PP

                         TIGR00465  78 aeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtgeakeiAlay 154
                                       aeikp+lk g+allf+HGfni+f qi++pkdvdv+++APKgpG+lvR++y eg Gvp l+A++qd+tg+a+e+Alay
  lcl|FitnessBrowser__Miya:8499378  91 AEIKPNLKPGDALLFAHGFNIHFGQIEPPKDVDVFMIAPKGPGHLVRRTYTEGGGVPCLVAIHQDATGKAMEKALAY 167
                                       ***************************************************************************** PP

                         TIGR00465 155 AkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelklivdllkekGle 231
                                       Ak++Ggar gv+ettFkeE+e+DLfGEqavLcGgl+ lika+f+tLveaGyqpe+Ayfe++he+klivdl++e+Gl+
  lcl|FitnessBrowser__Miya:8499378 168 AKGVGGARSGVIETTFKEETETDLFGEQAVLCGGLSSLIKAGFETLVEAGYQPEIAYFECLHEVKLIVDLIYEGGLA 244
                                       ***************************************************************************** PP

                         TIGR00465 232 lmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeearkkekeqeiekvGkelr 307
                                       +mr+++s+tA++g++ ++ +i++ee+kkem+k+l+eiq+G+fa++++le +ag+p f+++r+ e +++ie+vG +lr
  lcl|FitnessBrowser__Miya:8499378 245 KMRHSISDTAEYGDYVTGrRIVNEETKKEMKKVLQEIQEGTFARNFILEAKAGYPGFKATRRIEADHQIEQVGGKLR 321
                                       ***************9998********************************************************** PP

                         TIGR00465 308 alvka 312
                                        ++++
  lcl|FitnessBrowser__Miya:8499378 322 GMMPW 326
                                       ***98 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.08
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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