Alignments for a candidate for ilvC in Desulfovibrio zosterae DSM 11974

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Desulfovibrio zosterae DSM 11974

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_027723029.1 H589_RS0116415 ketol-acid reductoisomerase

Query= SwissProt::K4LVZ1
         (332 letters)



>NCBI__GCF_000425265.1:WP_027723029.1
          Length = 331

 Score =  257 bits (656), Expect = 3e-73
 Identities = 143/319 (44%), Positives = 194/319 (60%), Gaps = 7/319 (2%)

Query: 2   KIYYDQDADLQYLDGKTVAVIGYGSQGHAQSQNLRDSGVKVVVA--DIPSSENWKKAEEA 59
           KIY D+D D+  LDGKTVAVIGYGSQG AQS N+R+SGVKV+V   D     +W KAE  
Sbjct: 8   KIYRDEDVDMSVLDGKTVAVIGYGSQGRAQSMNMRESGVKVIVGAGDRTRHSSWDKAEAD 67

Query: 60  QFQPLTADEAAREADIIQILVPDEKQAALYRESIAPNLRPGKALVFSHGFNIHFKQIVPP 119
            F+  + ++A  +ADI+ IL+ D  Q  +Y ESI  NLRPG+ L F+HGF I +  I PP
Sbjct: 68  GFEVFSIEKAVEKADIVHILLQDPAQPPVYYESIHANLRPGQTLSFAHGFAILYGTIRPP 127

Query: 120 PDVDVFMVAPKGPGHLVRRMYEEGAGVPSLVAVEQDYSGQALNLALAYAKGIGATRAGVI 179
            D+DV +  P GPG + R+ Y++G+G+   V+V+QD SG A   ALA AK +G+TR G +
Sbjct: 128 KDIDVVLFVPNGPGPVTRQKYKDGSGIWGCVSVDQDVSGHAQETALAIAKAVGSTRVGAV 187

Query: 180 QTTFKEETETDLFGEQAVLCGGITELIRAGFDTLVDAGYQPEIAYFECLHEMKLIVDLIY 239
             TF+ ETE D + EQ VL GG   L+R  ++ +V  GY    AY + +  ++ I+D I 
Sbjct: 188 AMTFQHETEGDNYEEQ-VLYGGTIHLMRTMYNIMVKNGYPRSFAYAKAIRSIRSIIDDID 246

Query: 240 EGGI-STMRYSISDTAEYGDLTRGKRIITEATREEMKKILKEIQDGVFAREWLLENQVGR 298
           E GI S +    S T E+     G R+I E   EEM+KI +E + G FA+ WL E  +G 
Sbjct: 247 EVGIESYLTSRASRTCEFAVRHSGPRVINE---EEMEKIFEETESGTFAKNWLQEFSLGM 303

Query: 299 PVYNALRRKEQNHLIETVG 317
           P  N +RR      +E  G
Sbjct: 304 PTLNRIRRTWAESDMEQTG 322


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: 279
Number of extensions: 9
Number of successful extensions: 4
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 WP_027723029.1 H589_RS0116415 (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.15110.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.6e-92  295.1   0.0      3e-92  294.9   0.0    1.0  1  lcl|NCBI__GCF_000425265.1:WP_027723029.1  H589_RS0116415 ketol-acid reduct


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000425265.1:WP_027723029.1  H589_RS0116415 ketol-acid reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  294.9   0.0     3e-92     3e-92       1     309 [.      20     328 ..      20     331 .] 0.95

  Alignments for each domain:
  == domain 1  score: 294.9 bits;  conditional E-value: 3e-92
                                 TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkea..aswkkAeedGfkvltveeaikkadlimiLl 67 
                                               l+gk+va+iGyGsqG+aq++n+r+sg++vivg    +  +sw+kAe dGf+v+++e a++kad+++iLl
  lcl|NCBI__GCF_000425265.1:WP_027723029.1  20 LDGKTVAVIGYGSQGRAQSMNMRESGVKVIVGAGDRTrhSSWDKAEADGFEVFSIEKAVEKADIVHILL 88 
                                               689****************************98655555****************************** PP

                                 TIGR00465  68 pDevqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsl 136
                                                D +q+ vy ++i+ +l+ g++l+f+HGf i + +i++pkd+dvvl  P gpG + R++yk g G+ + 
  lcl|NCBI__GCF_000425265.1:WP_027723029.1  89 QDPAQPPVYYESIHANLRPGQTLSFAHGFAILYGTIRPPKDIDVVLFVPNGPGPVTRQKYKDGSGIWGC 157
                                               ********************************************************************* PP

                                 TIGR00465 137 iAveqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGy 205
                                               + v qdv+g+a+e+Ala+Aka+G++r+g +  tF++E+e D + Eq vL Gg   l+++ ++ +v++Gy
  lcl|NCBI__GCF_000425265.1:WP_027723029.1 158 VSVDQDVSGHAQETALAIAKAVGSTRVGAVAMTFQHETEGDNYEEQ-VLYGGTIHLMRTMYNIMVKNGY 225
                                               *******************************************998.57788888999*********** PP

                                 TIGR00465 206 qpelAyfeivhelklivdllkekGle.lmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGef 272
                                                 + Ay + +  +++i+d + e G+e ++ ++ s t ++   +++ ++++e   +em+ki++e+++G+f
  lcl|NCBI__GCF_000425265.1:WP_027723029.1 226 PRSFAYAKAIRSIRSIIDDIDEVGIEsYLTSRASRTCEFAVRHSGpRVINE---EEMEKIFEETESGTF 291
                                               *************************8468999*******999999777776...69************* PP

                                 TIGR00465 273 akewalekeagkpafeearkkekeqeiekvGkelral 309
                                               ak+w+ e++ g p+++++r++  e ++e++Gk  r+ 
  lcl|NCBI__GCF_000425265.1:WP_027723029.1 292 AKNWLQEFSLGMPTLNRIRRTWAESDMEQTGKIWREK 328
                                               ********************************99876 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 9.40
//
[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