GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvC in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_1540 Ketol-acid reductoisomerase (EC 1.1.1.86)

Query= SwissProt::Q9HVA2
         (338 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1540 Ketol-acid
           reductoisomerase (EC 1.1.1.86)
          Length = 338

 Score =  624 bits (1609), Expect = 0.0
 Identities = 312/338 (92%), Positives = 322/338 (95%)

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

Query: 61  LKVADVKTAVAAADVVMILTPDEFQGRLYKEEIEPNLKKGATLAFAHGFSIHYNQVVPRA 120
           LKV DV +AVAAAD+VMILTPDEFQ  LYK EIEPN+KKGATLAF+HGF+IHYNQVVPRA
Sbjct: 61  LKVTDVASAVAAADLVMILTPDEFQSSLYKNEIEPNIKKGATLAFSHGFAIHYNQVVPRA 120

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

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

Query: 241 GGIANMNYSISNNAEYGEYVTGPEVINAESRAAMRNALKRIQDGEYAKMFITEGAANYPS 300
           GGIANMNYSISNNAEYGEYVTGPEVINAESR AMRNALKRIQDGEYAKMFI+EGA  YPS
Sbjct: 241 GGIANMNYSISNNAEYGEYVTGPEVINAESRQAMRNALKRIQDGEYAKMFISEGATGYPS 300

Query: 301 MTAYRRNNAAHPIEQIGEKLRAMMPWIAANKIVDKSKN 338
           MTA RRNNAAH IE IGE+LR+MMPWI ANKIVDK+KN
Sbjct: 301 MTAKRRNNAAHGIEIIGEQLRSMMPWIGANKIVDKAKN 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: 5
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 PfGW456L13_1540 (Ketol-acid reductoisomerase (EC 1.1.1.86))
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.18672.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   2.8e-133  429.7   1.9   3.2e-133  429.5   1.9    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1540  Ketol-acid reductoisomerase (EC 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1540  Ketol-acid reductoisomerase (EC 1.1.1.86)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  429.5   1.9  3.2e-133  3.2e-133       1     312 [.      14     326 ..      14     328 .. 0.99

  Alignments for each domain:
  == domain 1  score: 429.5 bits;  conditional E-value: 3.2e-133
                                               TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltvee 55 
                                                             ++gkkvaiiGyGsqG+aqa nl+dsg++v+vglrk++a+++kAe  G+kv++v+ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1540  14 IQGKKVAIIGYGSQGHAQACNLKDSGVDVTVGLRKGSATVAKAEAHGLKVTDVAS 68 
                                                             689**************************************************** PP

                                               TIGR00465  56 aikkadlimiLlpDevqkevyeaeikpllkegkallfsHGfnivfkqivipkdvd 110
                                                             a+++adl+miL+pDe q++ y++ei+p++k+g++l fsHGf i+++q+v+++d+d
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1540  69 AVAAADLVMILTPDEFQSSLYKNEIEPNIKKGATLAFSHGFAIHYNQVVPRADLD 123
                                                             ******************************************************* PP

                                               TIGR00465 111 vvlvAPKgpGalvReeykegrGvpsliAveqdvtgeakeiAlayAkaiGgaragv 165
                                                             v+++APK+pG++vR+e+ +g G+p liA++qd++g+ak++Al+yA+++Gg+r g+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1540 124 VIMIAPKAPGHTVRSEFVKGGGIPDLIAIYQDASGNAKNVALSYAAGVGGGRTGI 178
                                                             ******************************************************* PP

                                               TIGR00465 166 lettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelkl 220
                                                             +ettFk+E+e+DLfGEqavLcGg  +l+ka+f+tLveaGy+pe+Ayfe++helkl
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1540 179 IETTFKDETETDLFGEQAVLCGGTVELVKAGFETLVEAGYAPEMAYFECLHELKL 233
                                                             ******************************************************* PP

                                               TIGR00465 221 ivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefak 274
                                                             ivdl++e+G+++m  ++sn A++g++ ++ e++++e +++m++ lk iq+Ge+ak
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1540 234 IVDLMYEGGIANMNYSISNNAEYGEYVTGpEVINAESRQAMRNALKRIQDGEYAK 288
                                                             *****************************9************************* PP

                                               TIGR00465 275 ewalekeagkpafeearkkekeqeiekvGkelralvka 312
                                                              ++ e ++g+p+++++r+ +  + ie +G++lr ++++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1540 289 MFISEGATGYPSMTAKRRNNAAHGIEIIGEQLRSMMPW 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: 8.83
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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