Alignments for a candidate for ilvC in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Escherichia coli BW25113

Align ketol-acid reductoisomerase [NAD(P)+] (EC 1.1.1.383); ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate 17826 b3774 ketol-acid reductoisomerase (NCBI)

Query= BRENDA::P05793
         (491 letters)



>FitnessBrowser__Keio:17826
          Length = 491

 Score =  978 bits (2527), Expect = 0.0
 Identities = 491/491 (100%), Positives = 491/491 (100%)

Query: 1   MANYFNTLNLRQQLAQLGKCRFMGRDEFADGASYLQGKKVVIVGCGAQGLNQGLNMRDSG 60
           MANYFNTLNLRQQLAQLGKCRFMGRDEFADGASYLQGKKVVIVGCGAQGLNQGLNMRDSG
Sbjct: 1   MANYFNTLNLRQQLAQLGKCRFMGRDEFADGASYLQGKKVVIVGCGAQGLNQGLNMRDSG 60

Query: 61  LDISYALRKEAIAEKRASWRKATENGFKVGTYEELIPQADLVINLTPDKQHSDVVRTVQP 120
           LDISYALRKEAIAEKRASWRKATENGFKVGTYEELIPQADLVINLTPDKQHSDVVRTVQP
Sbjct: 61  LDISYALRKEAIAEKRASWRKATENGFKVGTYEELIPQADLVINLTPDKQHSDVVRTVQP 120

Query: 121 LMKDGAALGYSHGFNIVEVGEQIRKDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPE 180
           LMKDGAALGYSHGFNIVEVGEQIRKDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPE
Sbjct: 121 LMKDGAALGYSHGFNIVEVGEQIRKDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPE 180

Query: 181 NDPKGEGMAIAKAWAAATGGHRAGVLESSFVAEVKSDLMGEQTILCGMLQAGSLLCFDKL 240
           NDPKGEGMAIAKAWAAATGGHRAGVLESSFVAEVKSDLMGEQTILCGMLQAGSLLCFDKL
Sbjct: 181 NDPKGEGMAIAKAWAAATGGHRAGVLESSFVAEVKSDLMGEQTILCGMLQAGSLLCFDKL 240

Query: 241 VEEGTDPAYAEKLIQFGWETITEALKQGGITLMMDRLSNPAKLRAYALSEQLKEIMAPLF 300
           VEEGTDPAYAEKLIQFGWETITEALKQGGITLMMDRLSNPAKLRAYALSEQLKEIMAPLF
Sbjct: 241 VEEGTDPAYAEKLIQFGWETITEALKQGGITLMMDRLSNPAKLRAYALSEQLKEIMAPLF 300

Query: 301 QKHMDDIISGEFSSGMMADWANDDKKLLTWREETGKTAFETAPQYEGKIGEQEYFDKGVL 360
           QKHMDDIISGEFSSGMMADWANDDKKLLTWREETGKTAFETAPQYEGKIGEQEYFDKGVL
Sbjct: 301 QKHMDDIISGEFSSGMMADWANDDKKLLTWREETGKTAFETAPQYEGKIGEQEYFDKGVL 360

Query: 361 MIAMVKAGVELAFETMVDSGIIEESAYYESLHELPLIANTIARKRLYEMNVVISDTAEYG 420
           MIAMVKAGVELAFETMVDSGIIEESAYYESLHELPLIANTIARKRLYEMNVVISDTAEYG
Sbjct: 361 MIAMVKAGVELAFETMVDSGIIEESAYYESLHELPLIANTIARKRLYEMNVVISDTAEYG 420

Query: 421 NYLFSYACVPLLKPFMAELQPGDLGKAIPEGAVDNGQLRDVNEAIRSHAIEQVGKKLRGY 480
           NYLFSYACVPLLKPFMAELQPGDLGKAIPEGAVDNGQLRDVNEAIRSHAIEQVGKKLRGY
Sbjct: 421 NYLFSYACVPLLKPFMAELQPGDLGKAIPEGAVDNGQLRDVNEAIRSHAIEQVGKKLRGY 480

Query: 481 MTDMKRIAVAG 491
           MTDMKRIAVAG
Sbjct: 481 MTDMKRIAVAG 491


Lambda     K      H
   0.317    0.135    0.390 

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: 941
Number of extensions: 21
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: 491
Length of database: 491
Length adjustment: 34
Effective length of query: 457
Effective length of database: 457
Effective search space:   208849
Effective search space used:   208849
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: 52 (24.6 bits)

Align candidate 17826 b3774 (ketol-acid reductoisomerase (NCBI))
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.2140820.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                   -----------
   4.8e-155  501.2   0.2   2.3e-141  456.2   0.2    2.0  2  FitnessBrowser__Keio:17826  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Keio:17826  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.2   0.2  2.3e-141  2.3e-141       1     313 [.      35     368 ..      35     369 .. 0.99
   2 !   48.6   0.0   2.9e-17   2.9e-17     186     311 ..     362     482 ..     361     485 .. 0.92

  Alignments for each domain:
  == domain 1  score: 456.2 bits;  conditional E-value: 2.3e-141
                   TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkea.....aswkkAeedGfkvltveeaikkadlimiLlpDevqkevyea 78 
                                 l+gkkv+i+G+G+qG +q+ln+rdsgl+++++lrkea     asw+kA+e+Gfkv t+ee+i++adl+++L+pD+ q++++++
  FitnessBrowser__Keio:17826  35 LQGKKVVIVGCGAQGLNQGLNMRDSGLDISYALRKEAiaekrASWRKATENGFKVGTYEELIPQADLVINLTPDK-QHSDVVR 116
                                 79*************************************************************************.9999999 PP

                   TIGR00465  79 eikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqd..vtgeakeiAlayAkaiG 159
                                 +++pl+k+g+al++sHGfniv+++++i+kd++vv+vAPK+pG++vReeyk+g+Gvp+liAv+++  ++ge+++iA+a+A+a+G
  FitnessBrowser__Keio:17826 117 TVQPLMKDGAALGYSHGFNIVEVGEQIRKDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPEndPKGEGMAIAKAWAAATG 199
                                 9************************************************************98877***************** PP

                   TIGR00465 160 garagvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelklivdllkekGlelmrdavsntAk 242
                                 g+ragvle++F++Ev+sDL+GEq++LcG+l+a+++++fd+Lve+G++p++A+++i++++++i+++lk++G++lm+d++sn+Ak
  FitnessBrowser__Keio:17826 200 GHRAGVLESSFVAEVKSDLMGEQTILCGMLQAGSLLCFDKLVEEGTDPAYAEKLIQFGWETITEALKQGGITLMMDRLSNPAK 282
                                 *********************************************************************************** PP

                   TIGR00465 243 lgalelreilkeelkkemqkilkeiqnGefak....ewalek........eagkpafeearkke...keqeiekvGkelralv 310
                                 l+a++l+e+lke +++ +qk++++i++Gef++    +wa+++        e+gk+afe+a+++e    eqe++++G+ ++a+v
  FitnessBrowser__Keio:17826 283 LRAYALSEQLKEIMAPLFQKHMDDIISGEFSSgmmaDWANDDkklltwreETGKTAFETAPQYEgkiGEQEYFDKGVLMIAMV 365
                                 *******************************99999*****9**********************9999*************** PP

                   TIGR00465 311 kae 313
                                 ka+
  FitnessBrowser__Keio:17826 366 KAG 368
                                 975 PP

  == domain 2  score: 48.6 bits;  conditional E-value: 2.9e-17
                   TIGR00465 186 cGglealikaafdtLveaGyqpelAyfeivhelklivdllkekGlelmrdavsntAklgalelreilkeelkkemqkilkeiq 268
                                 + +++a++++af+t+v+ G  +e Ay e +hel li++ + +k l +m   +s+tA++g++     ++ +  + ++  + e+q
  FitnessBrowser__Keio:17826 362 IAMVKAGVELAFETMVDSGIIEESAYYESLHELPLIANTIARKRLYEMNVVISDTAEYGNYL----FSYACVPLLKPFMAELQ 440
                                 5699*******************************************************986....5566778888888999* PP

                   TIGR00465 269 nGefakewalekeagkpafeearkkekeqeiekvGkelralvk 311
                                  G+  k  + e ++++ ++++ +++ + + ie+vGk+lr  + 
  FitnessBrowser__Keio:17826 441 PGDLGK-AIPEGAVDNGQLRDVNEAIRSHAIEQVGKKLRGYMT 482
                                 ******.7888899************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (491 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: 11.83
//
[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 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