Alignments for a candidate for proB in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Pseudomonas fluorescens GW456-L13

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate PfGW456L13_1472 Glutamate 5-kinase (EC 2.7.2.11) / RNA-binding C-terminal domain PUA

Query= BRENDA::P0A7B5
         (367 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1472
          Length = 368

 Score =  300 bits (769), Expect = 3e-86
 Identities = 161/366 (43%), Positives = 231/366 (63%), Gaps = 1/366 (0%)

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

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

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

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

Query: 241 VIGDVMEGISVGTLFHAQATPLENRKRWIFG-APPAGEITVDEGATAAILERGSSLLPKG 299
           V+  +  G  +GTL   +   L  RK+W+ G     G + +D GA  A+ +   SLLP G
Sbjct: 241 VLDRLKAGERIGTLLSPERGMLAARKQWLAGHLQTRGTLVLDAGAVTALSQGNKSLLPVG 300

Query: 300 IKSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAV 359
           +K V G+F RGE++     +GR+IA G++ Y++   ++I G  S+ I  +LGY   P  V
Sbjct: 301 VKLVQGSFRRGEMVVCVAPDGREIARGLANYSALEAQKIIGQSSEAIVGLLGYMAEPELV 360

Query: 360 HRDDMI 365
           HRD++I
Sbjct: 361 HRDNLI 366


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: 358
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: 368
Length adjustment: 30
Effective length of query: 337
Effective length of database: 338
Effective search space:   113906
Effective search space used:   113906
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_1472 (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.13404.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   2.4e-134  434.0   0.4   2.7e-134  433.8   0.4    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1472  Glutamate 5-kinase (EC 2.7.2.11)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1472  Glutamate 5-kinase (EC 2.7.2.11) / RNA-binding C-terminal dom
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  433.8   0.4  2.7e-134  2.7e-134       2     362 ..       6     366 ..       5     367 .. 0.99

  Alignments for each domain:
  == domain 1  score: 433.8 bits;  conditional E-value: 2.7e-134
                                               TIGR01027   2 riVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaL 56 
                                                             r VvK+Gs++Lt++ + l+r+ +   veq+ +l++aG e+v+vsSGavaaG+++L
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1472   6 RWVVKIGSALLTADGKGLDRAAMGVWVEQMVALHEAGVELVLVSSGAVAAGMSRL 60 
                                                             78***************************************************** PP

                                               TIGR01027  57 glperpkklaekQalaaVGQgrLmklyeklfsqyglkvaQiLLtradlskreryl 111
                                                             g ++rp  ++e Qa+aa+GQ  L++++e++f+++g+++aQiLLt++dls+r+ryl
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1472  61 GWTSRPSAMHELQAAAAIGQMGLVQAWESSFAKHGRHTAQILLTHDDLSDRKRYL 115
                                                             ******************************************************* PP

                                               TIGR01027 112 NarntleellelgvvpivNENDtvaveeikfGDNDtLsalvaalveAdlLvlltd 166
                                                             Nar+tl++l+el+v+p++NENDtv ++ei+fGDNDtL+alva+lveAdlLv+ltd
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1472 116 NARSTLRALVELKVIPVINENDTVVTDEIRFGDNDTLAALVANLVEADLLVILTD 170
                                                             ******************************************************* PP

                                               TIGR01027 167 vdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaaelAs 221
                                                              dg++dadpr+npdA+li e ++ + +l+avag++g ++G GGm+tKl aa+lA+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1472 171 RDGMFDADPRNNPDAQLIYEARADDPALDAVAGGTGGALGRGGMQTKLRAARLAA 225
                                                             ******************************************************* PP

                                               TIGR01027 222 ragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkii 276
                                                             r+g ++ii+ g+ +  + +l +++ +gtl+ +++  l +rkqw++ +++++G+++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1472 226 RSGAHTIIVGGRLERVLDRLKAGERIGTLLSPERGMLAARKQWLAGHLQTRGTLV 280
                                                             *************999*************************************** PP

                                               TIGR01027 277 vdegaeeallekgksLlpagvvevegnFsrgevveilaeegqeigkglvnyssee 331
                                                             +d+ga++al++ +ksLlp+gv  v+g+F+rge+v ++a++g+ei++gl+nys+ e
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1472 281 LDAGAVTALSQGNKSLLPVGVKLVQGSFRRGEMVVCVAPDGREIARGLANYSALE 335
                                                             ******************************************************* PP

                                               TIGR01027 332 lekikglkseeiedvLgyekkeevvhrdnlv 362
                                                              +ki g++se i  +Lgy  + e vhrdnl+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1472 336 AQKIIGQSSEAIVGLLGYMAEPELVHRDNLI 366
                                                             *****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (368 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 0.02s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 6.26
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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