Alignments for a candidate for ilvC in Acidimicrobium ferrooxidans DSM 10331

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Acidimicrobium ferrooxidans DSM 10331

Align ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate WP_218914812.1 AFER_RS08010 ketol-acid reductoisomerase

Query= BRENDA::D3PT81
         (339 letters)



>NCBI__GCF_000023265.1:WP_218914812.1
          Length = 337

 Score =  400 bits (1027), Expect = e-116
 Identities = 203/335 (60%), Positives = 253/335 (75%), Gaps = 1/335 (0%)

Query: 3   IYYDQDADIGFIKDKTVAILGFGSQGHAHALNLRDSGIKVVVGLRPGSRNEEKARKAGLE 62
           +YYD+DA+   I D+ VAI+G+GSQGHAHALNL DSG+ V VGLR GS + +KAR +GLE
Sbjct: 1   MYYDKDANPALITDRRVAIIGYGSQGHAHALNLLDSGVPVRVGLREGSASADKARASGLE 60

Query: 63  VLPVGEAVRRADVVMILLPDETQGAVYKAEVEPNLKEGAALAFAHGFNIHFGQIKPRRDL 122
           V  V +AVR AD+VM+L+PD T   +++ +V PNL+ G+A+AFAHGFNI FG I+P   +
Sbjct: 61  VSSVADAVRWADLVMLLVPDTTAPTLWREQVAPNLQPGSAVAFAHGFNIRFGLIEPDPSV 120

Query: 123 DVWMVAPKGPGHLVRSEYEKGSGVPSLVAVYQDASGSAFPTALAYAKANGGTRAGTIATT 182
           DV M+APKGPGHL+R  YE+G G+PSL+AV  DASG A  TALAYA A G TRAG + TT
Sbjct: 121 DVIMIAPKGPGHLLRRTYEEGGGIPSLIAVANDASGRAHDTALAYAWAIGSTRAGVLDTT 180

Query: 183 FKDETETDLFGEQTVLCGGLTQLIAAGFETLVEAGYPPEMAYFECLHEVKLIVDLIYESG 242
           F +ETETDLFGEQ VLCGGL+QL+ AGF+TLVEAGY PE AYFECLHE+KLIVDL+YE G
Sbjct: 181 FAEETETDLFGEQVVLCGGLSQLVRAGFDTLVEAGYQPESAYFECLHELKLIVDLLYEHG 240

Query: 243 FAGMRYSISNTAEYGDYTRGPMVINREETKARMREVLRQIQQGEFAREWMLENVVGQPTL 302
            +GM +S+S TAEYG  TRGP ++N +ET+A MR VL +I+ G FA E + E   G+P  
Sbjct: 241 LSGMWFSVSETAEYGGLTRGPRIVN-DETRAEMRRVLDEIRSGAFASELVDEIAAGRPRF 299

Query: 303 NANRNYWKDHPIEQVGPKLRAMMPFLKSRFTKEEV 337
            A R   ++  IEQVG  LRAMMPFL S    ++V
Sbjct: 300 EALRREAREAQIEQVGRDLRAMMPFLASATKLDQV 334


Lambda     K      H
   0.318    0.136    0.398 

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: 390
Number of extensions: 16
Number of successful extensions: 2
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: 339
Length of database: 337
Length adjustment: 28
Effective length of query: 311
Effective length of database: 309
Effective search space:    96099
Effective search space used:    96099
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_218914812.1 AFER_RS08010 (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.1131079.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.1e-133  428.2   0.0   9.4e-133  428.0   0.0    1.0  1  NCBI__GCF_000023265.1:WP_218914812.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000023265.1:WP_218914812.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  428.0   0.0  9.4e-133  9.4e-133       2     312 ..      13     324 ..      12     326 .. 0.99

  Alignments for each domain:
  == domain 1  score: 428.0 bits;  conditional E-value: 9.4e-133
                             TIGR00465   2 kgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqke 74 
                                            +++vaiiGyGsqG+a+alnl dsg+ v+vglr+++as +kA+  G++v +v++a++ adl+m L+pD++ ++
  NCBI__GCF_000023265.1:WP_218914812.1  13 TDRRVAIIGYGSQGHAHALNLLDSGVPVRVGLREGSASADKARASGLEVSSVADAVRWADLVMLLVPDTTAPT 85 
                                           6899********************************************************************* PP

                             TIGR00465  75 vyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtgea 147
                                            ++++++p+l+ g+a+ f+HGfni f  i++   vdv+++APKgpG+l+R++y+eg G+psliAv +d++g a
  NCBI__GCF_000023265.1:WP_218914812.1  86 LWREQVAPNLQPGSAVAFAHGFNIRFGLIEPDPSVDVIMIAPKGPGHLLRRTYEEGGGIPSLIAVANDASGRA 158
                                           ************************************************************************* PP

                             TIGR00465 148 keiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelkl 220
                                           +++AlayA aiG++ragvl+ttF eE+e+DLfGEq+vLcGgl++l++a+fdtLveaGyqpe Ayfe++helkl
  NCBI__GCF_000023265.1:WP_218914812.1 159 HDTALAYAWAIGSTRAGVLDTTFAEETETDLFGEQVVLCGGLSQLVRAGFDTLVEAGYQPESAYFECLHELKL 231
                                           ************************************************************************* PP

                             TIGR00465 221 ivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeeark 292
                                           ivdll+e+Gl++m+ +vs+tA++g+l+++ +i+++e+++em+ +l+ei++G fa+e + e +ag+p+fe+ r+
  NCBI__GCF_000023265.1:WP_218914812.1 232 IVDLLYEHGLSGMWFSVSETAEYGGLTRGpRIVNDETRAEMRRVLDEIRSGAFASELVDEIAAGRPRFEALRR 304
                                           ************************************************************************* PP

                             TIGR00465 293 kekeqeiekvGkelralvka 312
                                             +e +ie+vG++lra++++
  NCBI__GCF_000023265.1:WP_218914812.1 305 EAREAQIEQVGRDLRAMMPF 324
                                           *****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (337 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: 25.08
//
[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:

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 2024 update 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 original 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