Alignments for a candidate for ilvC in Acidithiobacillus ferrooxidans ATCC 23270

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Acidithiobacillus ferrooxidans ATCC 23270

Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate WP_012536329.1 AFE_RS03540 ketol-acid reductoisomerase

Query= metacyc::MONOMER-18814
         (338 letters)



>NCBI__GCF_000021485.1:WP_012536329.1
          Length = 338

 Score =  487 bits (1253), Expect = e-142
 Identities = 235/338 (69%), Positives = 282/338 (83%)

Query: 1   MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGVNVTVGLRKSGASWNKAANAG 60
           MKVFYD DADL+LI+ K V IIGYGSQGHAHALNLKDSGV+V VGLRK  +SW KA  AG
Sbjct: 1   MKVFYDNDADLALIQKKKVAIIGYGSQGHAHALNLKDSGVSVVVGLRKDSSSWEKAGKAG 60

Query: 61  LQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPRA 120
           L+VKEVA AV  ADVVMIL PDE    +Y++E+  NI++GAAL FAHGFN+H+G + PRA
Sbjct: 61  LEVKEVAAAVAAADVVMILTPDEGQGALYRDEIAPNIRQGAALVFAHGFNIHFGQIHPRA 120

Query: 121 DLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGIIE 180
           DLD  ++APK PGH VR+TYTQGGGVP LIAVHQ+ SG A +IALSYA ANGG RAG+IE
Sbjct: 121 DLDCFLVAPKGPGHLVRSTYTQGGGVPSLIAVHQDASGNATNIALSYAKANGGTRAGVIE 180

Query: 181 TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240
           T+FREETETDLFGEQAVLCGG   L++AGFETLVEAGYAPEMAYFEC+HELKLIVDL+YE
Sbjct: 181 TSFREETETDLFGEQAVLCGGATALVQAGFETLVEAGYAPEMAYFECMHELKLIVDLMYE 240

Query: 241 GGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAPT 300
           GGI+NM YSISN AEYG+   GPRVV  +TK  MK+ LT+IQ G++A+ F+LEN++G PT
Sbjct: 241 GGISNMRYSISNTAEYGDLTRGPRVVNADTKAEMKKILTEIQNGQFAREFILENQSGKPT 300

Query: 301 LISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338
           + + RR+ AEH IE VG+KLR+MM WI ++++VD+S+N
Sbjct: 301 MQAMRRIGAEHPIEVVGSKLRSMMTWIGQSRIVDRSRN 338


Lambda     K      H
   0.316    0.133    0.379 

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: 431
Number of extensions: 10
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: 338
Length of database: 338
Length adjustment: 28
Effective length of query: 310
Effective length of database: 310
Effective search space:    96100
Effective search space used:    96100
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_012536329.1 AFE_RS03540 (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.27667.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.3e-143  461.0   0.8   9.7e-143  460.8   0.8    1.0  1  lcl|NCBI__GCF_000021485.1:WP_012536329.1  AFE_RS03540 ketol-acid reductois


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021485.1:WP_012536329.1  AFE_RS03540 ketol-acid reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  460.8   0.8  9.7e-143  9.7e-143       1     312 [.      14     326 ..      14     328 .. 0.99

  Alignments for each domain:
  == domain 1  score: 460.8 bits;  conditional E-value: 9.7e-143
                                 TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 
                                               +++kkvaiiGyGsqG+a+alnl+dsg+ v+vglrk+++sw+kA + G++v++v+ a+++ad++miL+pD
  lcl|NCBI__GCF_000021485.1:WP_012536329.1  14 IQKKKVAIIGYGSQGHAHALNLKDSGVSVVVGLRKDSSSWEKAGKAGLEVKEVAAAVAAADVVMILTPD 82 
                                               689****************************************************************** PP

                                 TIGR00465  70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138
                                               e q + y+ ei+p++++g+al+f+HGfni+f qi++++d+d +lvAPKgpG+lvR++y +g GvpsliA
  lcl|NCBI__GCF_000021485.1:WP_012536329.1  83 EGQGALYRDEIAPNIRQGAALVFAHGFNIHFGQIHPRADLDCFLVAPKGPGHLVRSTYTQGGGVPSLIA 151
                                               ********************************************************************* PP

                                 TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207
                                               v+qd++g+a++iAl+yAka Gg+ragv+et+F+eE+e+DLfGEqavLcGg +al++a+f+tLveaGy+p
  lcl|NCBI__GCF_000021485.1:WP_012536329.1 152 VHQDASGNATNIALSYAKANGGTRAGVIETSFREETETDLFGEQAVLCGGATALVQAGFETLVEAGYAP 220
                                               ********************************************************************* PP

                                 TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275
                                               e+Ayfe++helklivdl++e+G+++mr ++sntA++g+l+++ +++++ +k+em+kil eiqnG+fa+e
  lcl|NCBI__GCF_000021485.1:WP_012536329.1 221 EMAYFECMHELKLIVDLMYEGGISNMRYSISNTAEYGDLTRGpRVVNADTKAEMKKILTEIQNGQFARE 289
                                               ********************************************************************* PP

                                 TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvka 312
                                               ++le++ gkp+++++r+   e+ ie vG++lr ++ +
  lcl|NCBI__GCF_000021485.1:WP_012536329.1 290 FILENQSGKPTMQAMRRIGAEHPIEVVGSKLRSMMTW 326
                                               **********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (338 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: 00:00:00.00
# Mc/sec: 11.97
//
[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