Alignments for a candidate for ilvC in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Pseudomonas putida KT2440

Align Ketol-acid reductoisomerase (NADP(+)); KARI; Acetohydroxy-acid isomeroreductase; AHIR; Alpha-keto-beta-hydroxylacyl reductoisomerase; Ketol-acid reductoisomerase type 1; Ketol-acid reductoisomerase type I; EC 1.1.1.86 (characterized)
to candidate PP_4678 PP_4678 Ketol-acid reductoisomerase

Query= SwissProt::Q9HVA2
         (338 letters)



>FitnessBrowser__Putida:PP_4678
          Length = 338

 Score =  631 bits (1627), Expect = 0.0
 Identities = 316/338 (93%), Positives = 325/338 (96%)

Query: 1   MRVFYDKDCDLSIIQGKKVAIIGYGSQGHAHACNLKDSGVDVTVGLRSGSATVAKAEAHG 60
           M+VFYDKDCDLSIIQGKKVAIIGYGSQGHA ACNLKDSGVDVTVGLR GSATVAKAEAHG
Sbjct: 1   MKVFYDKDCDLSIIQGKKVAIIGYGSQGHAQACNLKDSGVDVTVGLRKGSATVAKAEAHG 60

Query: 61  LKVADVKTAVAAADVVMILTPDEFQGRLYKEEIEPNLKKGATLAFAHGFSIHYNQVVPRA 120
           LKVADV TAVAAAD+VMILTPDEFQG LYK EIEPN+KKGATLAF+HGFSIHYNQVVPRA
Sbjct: 61  LKVADVATAVAAADLVMILTPDEFQGALYKNEIEPNIKKGATLAFSHGFSIHYNQVVPRA 120

Query: 121 DLDVIMIAPKAPGHTVRSEFVKGGGIPDLIAIYQDASGNAKNVALSYACGVGGGRTGIIE 180
           DLDVIMIAPKAPGHTVRSEFVKGGGIPDLIAIYQDASGNAKNVALSYA GVGGGRTGIIE
Sbjct: 121 DLDVIMIAPKAPGHTVRSEFVKGGGIPDLIAIYQDASGNAKNVALSYASGVGGGRTGIIE 180

Query: 181 TTFKDETETDLFGEQAVLCGGCVELVKAGFETLVEAGYAPEMAYFECLHELKLIVDLMYE 240
           TTFKDETETDLFGEQAVLCGG VELVKAGFETLVEAGYAPEMAYFECLHELKLIVDLMYE
Sbjct: 181 TTFKDETETDLFGEQAVLCGGTVELVKAGFETLVEAGYAPEMAYFECLHELKLIVDLMYE 240

Query: 241 GGIANMNYSISNNAEYGEYVTGPEVINAESRAAMRNALKRIQDGEYAKMFITEGAANYPS 300
           GGIANMNYSISNNAEYGEYVTGPEVIN ESR AMRNALKRIQDGEYAKMFI+EGA NYPS
Sbjct: 241 GGIANMNYSISNNAEYGEYVTGPEVINEESRKAMRNALKRIQDGEYAKMFISEGATNYPS 300

Query: 301 MTAYRRNNAAHPIEQIGEKLRAMMPWIAANKIVDKSKN 338
           MTA RRNNAAH IE IGE+LR+MMPWI+ANKIVDK+KN
Sbjct: 301 MTAKRRNNAAHGIEIIGEQLRSMMPWISANKIVDKTKN 338


Lambda     K      H
   0.317    0.134    0.389 

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: 493
Number of extensions: 6
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate PP_4678 PP_4678 (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.14059.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.3e-133  429.9   1.9   2.7e-133  429.7   1.9    1.0  1  lcl|FitnessBrowser__Putida:PP_4678  PP_4678 Ketol-acid reductoisomer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4678  PP_4678 Ketol-acid reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  429.7   1.9  2.7e-133  2.7e-133       1     312 [.      14     326 ..      14     328 .. 0.99

  Alignments for each domain:
  == domain 1  score: 429.7 bits;  conditional E-value: 2.7e-133
                           TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqkev 75 
                                         ++gkkvaiiGyGsqG+aqa nl+dsg++v+vglrk++a+++kAe  G+kv +v+ a+++adl+miL+pDe q + 
  lcl|FitnessBrowser__Putida:PP_4678  14 IQGKKVAIIGYGSQGHAQACNLKDSGVDVTVGLRKGSATVAKAEAHGLKVADVATAVAAADLVMILTPDEFQGAL 88 
                                         689************************************************************************ PP

                           TIGR00465  76 yeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtgeakei 150
                                         y++ei+p++k+g++l fsHGf+i+++q+v+++d+dv+++APK+pG++vR+e+ +g G+p liA++qd++g+ak++
  lcl|FitnessBrowser__Putida:PP_4678  89 YKNEIEPNIKKGATLAFSHGFSIHYNQVVPRADLDVIMIAPKAPGHTVRSEFVKGGGIPDLIAIYQDASGNAKNV 163
                                         *************************************************************************** PP

                           TIGR00465 151 AlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelklivdll 225
                                         Al+yA ++Gg+r g++ettFk+E+e+DLfGEqavLcGg  +l+ka+f+tLveaGy+pe+Ayfe++helklivdl+
  lcl|FitnessBrowser__Putida:PP_4678 164 ALSYASGVGGGRTGIIETTFKDETETDLFGEQAVLCGGTVELVKAGFETLVEAGYAPEMAYFECLHELKLIVDLM 238
                                         *************************************************************************** PP

                           TIGR00465 226 kekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeearkkekeqei 299
                                         +e+G+++m  ++sn A++g++ ++ e+++ee +k+m++ lk iq+Ge+ak ++ e ++++p+++++r+ +  + i
  lcl|FitnessBrowser__Putida:PP_4678 239 YEGGIANMNYSISNNAEYGEYVTGpEVINEESRKAMRNALKRIQDGEYAKMFISEGATNYPSMTAKRRNNAAHGI 313
                                         ************************9************************************************** PP

                           TIGR00465 300 ekvGkelralvka 312
                                         e +G++lr ++++
  lcl|FitnessBrowser__Putida:PP_4678 314 EIIGEQLRSMMPW 326
                                         ***********98 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: 00:00:00.01
# Mc/sec: 9.69
//
[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