GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvC in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_5177 Ketol-acid reductoisomerase (EC 1.1.1.86)

Query= SwissProt::Q9HVA2
         (338 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5177
          Length = 338

 Score =  629 bits (1622), Expect = 0.0
 Identities = 314/338 (92%), Positives = 326/338 (96%)

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

Query: 61  LKVADVKTAVAAADVVMILTPDEFQGRLYKEEIEPNLKKGATLAFAHGFSIHYNQVVPRA 120
           LKVADV +AVAAAD+VMILTPDEFQG LY++EIEPN+KKGATLAF+HGFSIHYNQVVPRA
Sbjct: 61  LKVADVASAVAAADLVMILTPDEFQGALYRDEIEPNIKKGATLAFSHGFSIHYNQVVPRA 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 MTAKRRNNAAHGIEIIGEQLRSMMPWISANKIVDKAKN 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: 503
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 Pf6N2E2_5177 (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.25631.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   6.4e-133  428.5   1.6   7.4e-133  428.3   1.6    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5177  Ketol-acid reductoisomerase (EC 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5177  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 !  428.3   1.6  7.4e-133  7.4e-133       1     312 [.      14     326 ..      14     328 .. 0.99

  Alignments for each domain:
  == domain 1  score: 428.3 bits;  conditional E-value: 7.4e-133
                                      TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlim 64 
                                                    ++gkkvaiiGyGsqG+aqa nl+dsg++v+vglrk++a+++kAe  G+kv +v+ a+++adl+m
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5177  14 IQGKKVAIIGYGSQGHAQACNLKDSGVDVTVGLRKGSATVAKAEAHGLKVADVASAVAAADLVM 77 
                                                    689************************************************************* PP

                                      TIGR00465  65 iLlpDevqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeyk 128
                                                    iL+pDe q + y+ ei+p++k+g++l fsHGf+i+++q+v+++d+dv+++APK+pG++vR+e+ 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5177  78 ILTPDEFQGALYRDEIEPNIKKGATLAFSHGFSIHYNQVVPRADLDVIMIAPKAPGHTVRSEFV 141
                                                    **************************************************************** PP

                                      TIGR00465 129 egrGvpsliAveqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGgleal 192
                                                    +g G+p liA++qd++g+ak++Al+yA+++Gg+r g++ettFk+E+e+DLfGEqavLcGg  +l
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5177 142 KGGGIPDLIAIYQDASGNAKNVALSYAAGVGGGRTGIIETTFKDETETDLFGEQAVLCGGTVEL 205
                                                    **************************************************************** PP

                                      TIGR00465 193 ikaafdtLveaGyqpelAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkee 255
                                                    +ka+f+tLveaGy+pe+Ayfe++helklivdl++e+G+++m  ++sn A++g++ ++ e++++e
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5177 206 VKAGFETLVEAGYAPEMAYFECLHELKLIVDLMYEGGIANMNYSISNNAEYGEYVTGpEVINAE 269
                                                    *********************************************************9****** PP

                                      TIGR00465 256 lkkemqkilkeiqnGefakewalekeagkpafeearkkekeqeiekvGkelralvka 312
                                                     +++m++ lk iq+Ge+ak ++ e ++g+p+++++r+ +  + ie +G++lr ++++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5177 270 SRQAMRNALKRIQDGEYAKMFISEGATGYPSMTAKRRNNAAHGIEIIGEQLRSMMPW 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.87
//
[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