Alignments for a candidate for proB in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Pseudomonas stutzeri RCH2

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate GFF3320 Psest_3384 glutamate 5-kinase

Query= BRENDA::P0A7B5
         (367 letters)



>FitnessBrowser__psRCH2:GFF3320
          Length = 372

 Score =  289 bits (739), Expect = 1e-82
 Identities = 158/366 (43%), Positives = 224/366 (61%), Gaps = 1/366 (0%)

Query: 1   MSDSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHL 60
           +S ++  VVK+G+++LT   R L++A +   V Q   L  AG  +V+V+SGA+AAG   L
Sbjct: 5   VSGARRWVVKIGSALLTADGRGLDQAAMAVWVDQMVALREAGVELVLVSSGAVAAGMSRL 64

Query: 61  GYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDT 120
           G+   P  +   Q  AAVGQ  LI+ WE  F+       Q+L+T  D+ DR+R+LNAR T
Sbjct: 65  GWSSRPKAVHELQAAAAVGQMGLIRAWESSFARCDQQTAQILVTHDDLSDRKRYLNARST 124

Query: 121 LRALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPR 180
           LR L+D  +VPVINEND V T EI+ GDND L AL A L  AD L++LTD+ G++ ADPR
Sbjct: 125 LRTLIDLGVVPVINENDTVVTDEIRFGDNDTLGALVANLVEADLLVILTDRDGMFDADPR 184

Query: 181 SNPQAELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPG 240
            NPQA LI +    D AL A+AG +   LG GGM TKL+AA +A R+G  T+I  G    
Sbjct: 185 FNPQANLISEARADDPALDAVAGGTGGALGRGGMQTKLRAARLAARSGAHTVIVGGRIEQ 244

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

Query: 300 IKSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAV 359
           +++V G F RGE++     +G ++A G+  Y++   +RI G  S EI+ +LGY   P  +
Sbjct: 305 VRAVQGAFRRGEMVVCVGPQGAEVARGLVNYSAAEAQRILGRPSDEIEKLLGYVDEPELI 364

Query: 360 HRDDMI 365
           HRD+MI
Sbjct: 365 HRDNMI 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: 368
Number of extensions: 18
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 GFF3320 Psest_3384 (glutamate 5-kinase)
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.5073.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.1e-134  435.1   0.1   1.2e-134  435.0   0.1    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3320  Psest_3384 glutamate 5-kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3320  Psest_3384 glutamate 5-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.0   0.1  1.2e-134  1.2e-134       2     362 ..      10     370 ..       9     371 .. 0.99

  Alignments for each domain:
  == domain 1  score: 435.0 bits;  conditional E-value: 1.2e-134
                           TIGR01027   2 riVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaaVGQ 76 
                                         r VvK+Gs++Lt++ + l+++ +a  v q+ +l++aG e+v+vsSGavaaG+++Lg ++rpk ++e Qa+aaVGQ
  lcl|FitnessBrowser__psRCH2:GFF3320  10 RWVVKIGSALLTADGRGLDQAAMAVWVDQMVALREAGVELVLVSSGAVAAGMSRLGWSSRPKAVHELQAAAAVGQ 84 
                                         67************************************************************************* PP

                           TIGR01027  77 grLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDtLsal 151
                                           L++++e++f++ ++++aQiL t++dls+r+rylNar+tl++l++lgvvp++NENDtv ++ei+fGDNDtL al
  lcl|FitnessBrowser__psRCH2:GFF3320  85 MGLIRAWESSFARCDQQTAQILVTHDDLSDRKRYLNARSTLRTLIDLGVVPVINENDTVVTDEIRFGDNDTLGAL 159
                                         *************************************************************************** PP

                           TIGR01027 152 vaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaaelAsragve 226
                                         va+lveAdlLv+ltd dg++dadpr np+A+li+e ++ + +l+avag++g ++G GGm+tKl aa+lA+r+g +
  lcl|FitnessBrowser__psRCH2:GFF3320 160 VANLVEADLLVILTDRDGMFDADPRFNPQANLISEARADDPALDAVAGGTGGALGRGGMQTKLRAARLAARSGAH 234
                                         *************************************************************************** PP

                           TIGR01027 227 viiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekgksLlpagvveve 301
                                         ++i+ g+ ++ +a+l +++ +gtl++++ ++  +rkqw++ +++++G++++d+ga++al++ ++sLlp+gv +v+
  lcl|FitnessBrowser__psRCH2:GFF3320 235 TVIVGGRIEQVLARLKAGERLGTLLAPECSRHAARKQWLAGHLQTRGTLTLDDGAVHALRQGNRSLLPVGVRAVQ 309
                                         *************************************************************************** PP

                           TIGR01027 302 gnFsrgevveilaeegqeigkglvnysseelekikglkseeiedvLgyekkeevvhrdnlv 362
                                         g F+rge+v ++ ++g+e+++glvnys++e ++i g++s+eie++Lgy ++ e +hrdn++
  lcl|FitnessBrowser__psRCH2:GFF3320 310 GAFRRGEMVVCVGPQGAEVARGLVNYSAAEAQRILGRPSDEIEKLLGYVDEPELIHRDNMI 370
                                         ***********************************************************98 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.80
//
[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