Alignments for a candidate for ilvC in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Burkholderia phytofirmans PsJN

Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate BPHYT_RS06555 BPHYT_RS06555 ketol-acid reductoisomerase

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



>FitnessBrowser__BFirm:BPHYT_RS06555
          Length = 338

 Score =  617 bits (1590), Expect = 0.0
 Identities = 308/338 (91%), Positives = 322/338 (95%)

Query: 1   MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGVNVTVGLRKSGASWNKAANAG 60
           MKVFYDKDADLSLIKGK VTIIGYGSQGHAHALNLK+SGVN+TVGLRK GASW+KA NAG
Sbjct: 1   MKVFYDKDADLSLIKGKQVTIIGYGSQGHAHALNLKESGVNITVGLRKGGASWSKAENAG 60

Query: 61  LQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPRA 120
           LQVKEVAEAVKGADVVM+LLPDEQIA+VY  EVH NIK+GAALAFAHGFNVHYG VIPRA
Sbjct: 61  LQVKEVAEAVKGADVVMMLLPDEQIAEVYAKEVHANIKQGAALAFAHGFNVHYGQVIPRA 120

Query: 121 DLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGIIE 180
           DLDVIMIAPKAPGHTVR TY+QGGGVPHLIAV Q+KSGAARDIALSYA ANGGGRAGIIE
Sbjct: 121 DLDVIMIAPKAPGHTVRGTYSQGGGVPHLIAVAQDKSGAARDIALSYAAANGGGRAGIIE 180

Query: 181 TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240
           TNFREETETDLFGEQAVLCGGTV+LIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE
Sbjct: 181 TNFREETETDLFGEQAVLCGGTVDLIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240

Query: 241 GGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAPT 300
           GGIANMNYSISNNAEYGEYVTGPR+VT ETKKAMK  LTDIQTGEYAKSF++ENKAGAPT
Sbjct: 241 GGIANMNYSISNNAEYGEYVTGPRIVTAETKKAMKAVLTDIQTGEYAKSFIIENKAGAPT 300

Query: 301 LISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338
           L SRRRLTAEHQIE VGAKLR+MMPWIA NK+VDQSKN
Sbjct: 301 LQSRRRLTAEHQIETVGAKLRSMMPWIAANKLVDQSKN 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: 547
Number of extensions: 16
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 BPHYT_RS06555 BPHYT_RS06555 (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.8596.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   4.1e-136  439.0   3.8   4.7e-136  438.8   3.8    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS06555  BPHYT_RS06555 ketol-acid reducto


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS06555  BPHYT_RS06555 ketol-acid reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.8   3.8  4.7e-136  4.7e-136       1     312 [.      14     326 ..      14     328 .. 0.99

  Alignments for each domain:
  == domain 1  score: 438.8 bits;  conditional E-value: 4.7e-136
                                TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDe 70 
                                              +kgk+v+iiGyGsqG+a+alnl++sg+n++vglrk++asw+kAe+ G++v++v+ea+k ad++m+LlpDe
  lcl|FitnessBrowser__BFirm:BPHYT_RS06555  14 IKGKQVTIIGYGSQGHAHALNLKESGVNITVGLRKGGASWSKAENAGLQVKEVAEAVKGADVVMMLLPDE 83 
                                              689******************************************************************* PP

                                TIGR00465  71 vqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAve 140
                                              +  evy +e++ ++k+g+al f+HGfn+++ q+ +++d+dv+++APK+pG++vR +y +g Gvp+liAv 
  lcl|FitnessBrowser__BFirm:BPHYT_RS06555  84 QIAEVYAKEVHANIKQGAALAFAHGFNVHYGQVIPRADLDVIMIAPKAPGHTVRGTYSQGGGVPHLIAVA 153
                                              ********************************************************************** PP

                                TIGR00465 141 qdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelA 210
                                              qd +g a++iAl+yA+a Gg+rag++et F+eE+e+DLfGEqavLcGg  +lika+f+tLveaGy+pe+A
  lcl|FitnessBrowser__BFirm:BPHYT_RS06555 154 QDKSGAARDIALSYAAANGGGRAGIIETNFREETETDLFGEQAVLCGGTVDLIKAGFETLVEAGYAPEMA 223
                                              ********************************************************************** PP

                                TIGR00465 211 yfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewale 279
                                              yfe++helklivdl++e+G+++m  ++sn A++g++ ++ +i+++e+kk+m+ +l +iq+Ge+ak +++e
  lcl|FitnessBrowser__BFirm:BPHYT_RS06555 224 YFECLHELKLIVDLIYEGGIANMNYSISNNAEYGEYVTGpRIVTAETKKAMKAVLTDIQTGEYAKSFIIE 293
                                              ***************************************9****************************** PP

                                TIGR00465 280 keagkpafeearkkekeqeiekvGkelralvka 312
                                              ++ag+p++++ r+   e++ie vG +lr ++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS06555 294 NKAGAPTLQSRRRLTAEHQIETVGAKLRSMMPW 326
                                              *******************************97 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.58
//
[ok]

This GapMind analysis is from Apr 09 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