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.18534.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  lcl|FitnessBrowser__Keio:17826  b3774 ketol-acid reductoisomeras


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17826  b3774 ketol-acid reductoisomerase (NCBI)
   #    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.....aswkkAeedGfkvltveeaikkadlimiLlpDevqke 74 
                                     l+gkkv+i+G+G+qG +q+ln+rdsgl+++++lrkea     asw+kA+e+Gfkv t+ee+i++adl+++L+pD+ q++
  lcl|FitnessBrowser__Keio:17826  35 LQGKKVVIVGCGAQGLNQGLNMRDSGLDISYALRKEAiaekrASWRKATENGFKVGTYEELIPQADLVINLTPDK-QHS 112
                                     79*************************************************************************.999 PP

                       TIGR00465  75 vyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqd..vtgeakeiA 151
                                     +++++++pl+k+g+al++sHGfniv+++++i+kd++vv+vAPK+pG++vReeyk+g+Gvp+liAv+++  ++ge+++iA
  lcl|FitnessBrowser__Keio:17826 113 DVVRTVQPLMKDGAALGYSHGFNIVEVGEQIRKDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPEndPKGEGMAIA 191
                                     99999************************************************************98877********* PP

                       TIGR00465 152 layAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelklivdllkekGl 230
                                     +a+A+a+Gg+ragvle++F++Ev+sDL+GEq++LcG+l+a+++++fd+Lve+G++p++A+++i++++++i+++lk++G+
  lcl|FitnessBrowser__Keio:17826 192 KAWAAATGGHRAGVLESSFVAEVKSDLMGEQTILCGMLQAGSLLCFDKLVEEGTDPAYAEKLIQFGWETITEALKQGGI 270
                                     ******************************************************************************* PP

                       TIGR00465 231 elmrdavsntAklgalelreilkeelkkemqkilkeiqnGefak....ewalek........eagkpafeearkke... 294
                                     +lm+d++sn+Akl+a++l+e+lke +++ +qk++++i++Gef++    +wa+++        e+gk+afe+a+++e   
  lcl|FitnessBrowser__Keio:17826 271 TLMMDRLSNPAKLRAYALSEQLKEIMAPLFQKHMDDIISGEFSSgmmaDWANDDkklltwreETGKTAFETAPQYEgki 349
                                     *******************************************99999*****9**********************999 PP

                       TIGR00465 295 keqeiekvGkelralvkae 313
                                      eqe++++G+ ++a+vka+
  lcl|FitnessBrowser__Keio:17826 350 GEQEYFDKGVLMIAMVKAG 368
                                     9***************975 PP

  == domain 2  score: 48.6 bits;  conditional E-value: 2.9e-17
                       TIGR00465 186 cGglealikaafdtLveaGyqpelAyfeivhelklivdllkekGlelmrdavsntAklgalelreilkeelkkemqkil 264
                                     + +++a++++af+t+v+ G  +e Ay e +hel li++ + +k l +m   +s+tA++g++     ++ +  + ++  +
  lcl|FitnessBrowser__Keio:17826 362 IAMVKAGVELAFETMVDSGIIEESAYYESLHELPLIANTIARKRLYEMNVVISDTAEYGNYL----FSYACVPLLKPFM 436
                                     5699*******************************************************986....5566778888888 PP

                       TIGR00465 265 keiqnGefakewalekeagkpafeearkkekeqeiekvGkelralvk 311
                                      e+q G+  k  + e ++++ ++++ +++ + + ie+vGk+lr  + 
  lcl|FitnessBrowser__Keio:17826 437 AELQPGDLGK-AIPEGAVDNGQLRDVNEAIRSHAIEQVGKKLRGYMT 482
                                     999*******.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: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 2.24
//
[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:

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