GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvC in Leptospirillum ferrooxidans C2-3

Align ketol-acid reductoisomerase (NAD+) (EC 1.1.1.382); ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate WP_014450633.1 LFE_RS12750 ketol-acid reductoisomerase

Query= BRENDA::C8WR67
         (344 letters)



>NCBI__GCF_000284315.1:WP_014450633.1
          Length = 339

 Score =  447 bits (1150), Expect = e-130
 Identities = 217/330 (65%), Positives = 262/330 (79%)

Query: 2   EKIYYDADISIQPLADKRIAVIGYGSQGHAHAQNLRDSGFDVVIGLRPGSSWAKAEADGF 61
           +KI Y++D++++ +  K++A+IG+GSQGHAHA NLR+S   V IGLRPG+SW KAE  GF
Sbjct: 3   KKISYESDLNLKLIQGKKVAIIGFGSQGHAHALNLRESAVSVEIGLRPGASWTKAEGFGF 62

Query: 62  RVMAVGEAVEESDVIMILLPDERQPAVYEREIRPYLTAGKALAFAHGFNIHFSQIQPPKD 121
           + + V EAV+++D +MILLPDE Q  +Y  EIRP L  G  LAF HGFNIHF QI PPKD
Sbjct: 63  KPVTVSEAVKKADFVMILLPDELQGDIYRDEIRPNLRPGMTLAFGHGFNIHFGQITPPKD 122

Query: 122 VDVFMVAPKGPGHLVRRVYEAGGGVPALIAVHQDASGQAKDLALAYARGIGAGRAGILTT 181
           VDV ++APKGPGHLVR  Y+ G GVPALIA+HQDA+  AKDLAL+YA  IG GR GI  T
Sbjct: 123 VDVMLIAPKGPGHLVRSEYQKGSGVPALIAIHQDATKTAKDLALSYAGAIGGGRPGIFET 182

Query: 182 TFREETETDLFGEQAVLCGGLSALIKAGFETLVEAGYQPEIAYFECLHEMKLIVDLIYEG 241
           TFREETETDLFGEQ VLCGGL+ALI AGFETL EAGY PE+AYFECLHE+KLIVDLIYEG
Sbjct: 183 TFREETETDLFGEQVVLCGGLTALITAGFETLTEAGYAPEMAYFECLHEVKLIVDLIYEG 242

Query: 242 GLEYMRYSISDTAQWGDFTSGPRIINEETKKEMRRILADIQSGAFAKSWILENQANRPMF 301
           G+  MRYSIS+TA++GD T GPRII  ETK EM++IL +IQSG FAK +ILEN+A RP+F
Sbjct: 243 GISNMRYSISNTAEYGDLTRGPRIITSETKAEMKKILHEIQSGQFAKEFILENKAGRPVF 302

Query: 302 NAINRRELEHPIEVVGRKLRSMMPFIKAKR 331
            A+ +    HPIE VG ++RSMMP+I   R
Sbjct: 303 QALEKSGQNHPIEKVGNEIRSMMPWIGKSR 332


Lambda     K      H
   0.320    0.138    0.404 

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: 396
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: 344
Length of database: 339
Length adjustment: 29
Effective length of query: 315
Effective length of database: 310
Effective search space:    97650
Effective search space used:    97650
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_014450633.1 LFE_RS12750 (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.885769.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-140  453.8   0.0   1.5e-140  453.6   0.0    1.0  1  NCBI__GCF_000284315.1:WP_014450633.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000284315.1:WP_014450633.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  453.6   0.0  1.5e-140  1.5e-140       1     312 [.      16     327 ..      16     329 .. 0.99

  Alignments for each domain:
  == domain 1  score: 453.6 bits;  conditional E-value: 1.5e-140
                             TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqk 73 
                                           ++gkkvaiiG+GsqG+a+alnlr+s + v +glr++ asw+kAe  Gfk +tv+ea+kkad++miLlpDe+q 
  NCBI__GCF_000284315.1:WP_014450633.1  16 IQGKKVAIIGFGSQGHAHALNLRESAVSVEIGLRPG-ASWTKAEGFGFKPVTVSEAVKKADFVMILLPDELQG 87 
                                           689*******************************98.9*********************************** PP

                             TIGR00465  74 evyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtge 146
                                           + y+ ei+p+l+ g +l f HGfni+f qi++pkdvdv+l+APKgpG+lvR+ey++g Gvp+liA++qd+t  
  NCBI__GCF_000284315.1:WP_014450633.1  88 DIYRDEIRPNLRPGMTLAFGHGFNIHFGQITPPKDVDVMLIAPKGPGHLVRSEYQKGSGVPALIAIHQDATKT 160
                                           ************************************************************************* PP

                             TIGR00465 147 akeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelk 219
                                           ak+ Al+yA aiGg+r g++ettF+eE+e+DLfGEq+vLcGgl+ali a+f+tL+eaGy+pe+Ayfe++he+k
  NCBI__GCF_000284315.1:WP_014450633.1 161 AKDLALSYAGAIGGGRPGIFETTFREETETDLFGEQVVLCGGLTALITAGFETLTEAGYAPEMAYFECLHEVK 233
                                           ************************************************************************* PP

                             TIGR00465 220 livdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeear 291
                                           livdl++e+G+++mr ++sntA++g+l+++ +i++ e+k+em+kil+eiq+G+fake++le++ag+p f++ +
  NCBI__GCF_000284315.1:WP_014450633.1 234 LIVDLIYEGGISNMRYSISNTAEYGDLTRGpRIITSETKAEMKKILHEIQSGQFAKEFILENKAGRPVFQALE 306
                                           ************************************************************************* PP

                             TIGR00465 292 kkekeqeiekvGkelralvka 312
                                           k+ +++ iekvG+e+r ++++
  NCBI__GCF_000284315.1:WP_014450633.1 307 KSGQNHPIEKVGNEIRSMMPW 327
                                           *******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (339 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: 00:00:00.00
# Mc/sec: 23.44
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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