GapMind for Amino acid biosynthesis

 

Aligments for a candidate for proB in Pseudomonas fluorescens FW300-N1B4

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate Pf1N1B4_2800 Glutamate 5-kinase (EC 2.7.2.11) / RNA-binding C-terminal domain PUA

Query= BRENDA::P0A7B5
         (367 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2800 Glutamate 5-kinase
           (EC 2.7.2.11) / RNA-binding C-terminal domain PUA
          Length = 372

 Score =  297 bits (761), Expect = 3e-85
 Identities = 161/366 (43%), Positives = 230/366 (62%), Gaps = 1/366 (0%)

Query: 1   MSDSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHL 60
           ++ +Q  VVK+G+++LT   + L+RA +   V Q   LH AG  +V+V+SGA+AAG   L
Sbjct: 5   VTGAQRWVVKIGSALLTADGKGLDRAAMGVWVEQMVALHEAGVELVLVSSGAVAAGMSRL 64

Query: 61  GYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDT 120
           G+   P+ +   Q  AA+GQ  L+Q WE  F+ +G H  Q+LLT  D+ DR+R+LNAR T
Sbjct: 65  GWTVRPSAMHELQAAAAIGQMGLVQAWESSFAEHGRHTAQILLTHDDLSDRKRYLNARST 124

Query: 121 LRALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPR 180
           LRAL++  ++PVINEND V T EI+ GDND L+AL A L  AD L++LTD+ G++ ADPR
Sbjct: 125 LRALVELKVIPVINENDTVVTDEIRFGDNDTLAALVANLVEADLLVILTDRDGMFDADPR 184

Query: 181 SNPQAELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPG 240
           +NP A+LI +    D AL A+AG +   LG GGM TKL+AA +A R+G  TII  G    
Sbjct: 185 NNPDAKLIYEARADDPALDAVAGSTGGALGRGGMQTKLRAARLAARSGAHTIIVGGRIDR 244

Query: 241 VIGDVMEGISVGTLFHAQATPLENRKRWIFG-APPAGEITVDEGATAAILERGSSLLPKG 299
           V+  +  G  +GTL   +   L  RK+W+ G     G + +D GA  A+     SLLP G
Sbjct: 245 VLDRLKAGERIGTLLSPERGMLAARKQWLAGHLQTRGTLVLDAGAVTALSLGNKSLLPVG 304

Query: 300 IKSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAV 359
           +K V G+F RGE++     +GR+IA G++ Y++   ++I G  S+ I  +LGY   P  V
Sbjct: 305 VKLVQGSFRRGEMVVCVAPDGREIARGLANYSALEAQKIIGQSSEAIVGLLGYMAEPELV 364

Query: 360 HRDDMI 365
           HRD++I
Sbjct: 365 HRDNLI 370


Lambda     K      H
   0.318    0.135    0.384 

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: 354
Number of extensions: 12
Number of successful extensions: 2
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: 367
Length of database: 372
Length adjustment: 30
Effective length of query: 337
Effective length of database: 342
Effective search space:   115254
Effective search space used:   115254
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 Pf1N1B4_2800 (Glutamate 5-kinase (EC 2.7.2.11) / RNA-binding C-terminal domain PUA)
to HMM TIGR01027 (proB: glutamate 5-kinase (EC 2.7.2.11))

# 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/TIGR01027.hmm
# target sequence database:        /tmp/gapView.26180.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01027  [M=363]
Accession:   TIGR01027
Description: proB: glutamate 5-kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
     4e-133  430.0   0.4   4.5e-133  429.8   0.4    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2800  Glutamate 5-kinase (EC 2.7.2.11)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2800  Glutamate 5-kinase (EC 2.7.2.11) / RNA-binding C-terminal domain PUA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  429.8   0.4  4.5e-133  4.5e-133       2     362 ..      10     370 ..       9     371 .. 0.99

  Alignments for each domain:
  == domain 1  score: 429.8 bits;  conditional E-value: 4.5e-133
                                      TIGR01027   2 riVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkkl 65 
                                                    r VvK+Gs++Lt++ + l+r+ +   veq+ +l++aG e+v+vsSGavaaG+++Lg + rp  +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2800  10 RWVVKIGSALLTADGKGLDRAAMGVWVEQMVALHEAGVELVLVSSGAVAAGMSRLGWTVRPSAM 73 
                                                    78************************************************************** PP

                                      TIGR01027  66 aekQalaaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpiv 129
                                                    +e Qa+aa+GQ  L++++e++f+++g+++aQiLLt++dls+r+rylNar+tl++l+el+v+p++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2800  74 HELQAAAAIGQMGLVQAWESSFAEHGRHTAQILLTHDDLSDRKRYLNARSTLRALVELKVIPVI 137
                                                    **************************************************************** PP

                                      TIGR01027 130 NENDtvaveeikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieee 193
                                                    NENDtv ++ei+fGDNDtL+alva+lveAdlLv+ltd dg++dadpr+npdAkli e ++ + +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2800 138 NENDTVVTDEIRFGDNDTLAALVANLVEADLLVILTDRDGMFDADPRNNPDAKLIYEARADDPA 201
                                                    **************************************************************** PP

                                      TIGR01027 194 lkavagssgssvGTGGmrtKleaaelAsragveviiasgekpekiadlledaavgtlfeakkkk 257
                                                    l+avags+g ++G GGm+tKl aa+lA+r+g ++ii+ g+    + +l +++ +gtl+ +++  
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2800 202 LDAVAGSTGGALGRGGMQTKLRAARLAARSGAHTIIVGGRIDRVLDRLKAGERIGTLLSPERGM 265
                                                    ****************************************999999999*************** PP

                                      TIGR01027 258 lknrkqwilaaseakGkiivdegaeeallekgksLlpagvvevegnFsrgevveilaeegqeig 321
                                                    l +rkqw++ +++++G++++d+ga++al+  +ksLlp+gv  v+g+F+rge+v ++a++g+ei+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2800 266 LAARKQWLAGHLQTRGTLVLDAGAVTALSLGNKSLLPVGVKLVQGSFRRGEMVVCVAPDGREIA 329
                                                    **************************************************************** PP

                                      TIGR01027 322 kglvnysseelekikglkseeiedvLgyekkeevvhrdnlv 362
                                                    +gl+nys+ e +ki g++se i  +Lgy  + e vhrdnl+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2800 330 RGLANYSALEAQKIIGQSSEAIVGLLGYMAEPELVHRDNLI 370
                                                    ***************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (372 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 6.90
//
[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