Alignments for a candidate for proB in Pseudomonas benzenivorans DSM 8628

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Pseudomonas benzenivorans DSM 8628

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate WP_090439933.1 BLS63_RS03675 glutamate 5-kinase

Query= BRENDA::P0A7B5
         (367 letters)



>NCBI__GCF_900100495.1:WP_090439933.1
          Length = 372

 Score =  297 bits (760), Expect = 4e-85
 Identities = 161/359 (44%), Positives = 227/359 (63%), Gaps = 1/359 (0%)

Query: 8   VVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHLGYPELPA 67
           VVK+G+++LT   R L+RA +   VRQ   L   G  +V+V+SGA+AAG   LG+   P+
Sbjct: 12  VVKIGSALLTADGRGLDRAAMAVWVRQMVALREQGVELVLVSSGAVAAGMSRLGWTARPS 71

Query: 68  TIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDTLRALLDN 127
            +   Q  AA+GQ  LIQ WE  F+ +G    Q+LLT  D+ DR+R+LNAR TLR L++ 
Sbjct: 72  AMHELQAAAAIGQMVLIQAWESSFAEHGRRTAQILLTHDDLSDRKRYLNARSTLRTLVEL 131

Query: 128 NIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPRSNPQAEL 187
           ++VPVINEND V T EI+ GDND L+AL A L  AD L++LTD+ G+Y ADPR NP AEL
Sbjct: 132 DVVPVINENDTVVTDEIRFGDNDTLAALVANLVEADLLVILTDRDGMYNADPRHNPGAEL 191

Query: 188 IKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPGVIGDVME 247
           I +    D AL A+AG     LG GGM TKL+AA +A R+G  T+I  G+   V+  +  
Sbjct: 192 IYEARADDPALDAVAGGVGGALGRGGMQTKLRAARLAARSGAHTVIVGGAIEQVLARLRS 251

Query: 248 GISVGTLFHAQATPLENRKRWIFG-APPAGEITVDEGATAAILERGSSLLPKGIKSVTGN 306
           G  +GTL   + + L  RK+W+ G     G + +D GA  A++    SLLP G+K+V G+
Sbjct: 252 GERLGTLLAPERSLLAARKQWLAGHLQTRGTLVLDAGAVKALVSDRKSLLPVGVKAVQGS 311

Query: 307 FSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAVHRDDMI 365
           F RGE++     +GR+IA G++ Y++   ++I G  S+ I+ +LGY   P  VHRD++I
Sbjct: 312 FRRGEMVVCVGPDGREIARGLANYSALEAQKIIGQSSEAIERLLGYVDEPELVHRDNLI 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: 359
Number of extensions: 14
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 WP_090439933.1 BLS63_RS03675 (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.4632.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-135  437.4   0.2   2.6e-135  437.2   0.2    1.0  1  lcl|NCBI__GCF_900100495.1:WP_090439933.1  BLS63_RS03675 glutamate 5-kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090439933.1  BLS63_RS03675 glutamate 5-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.2   0.2  2.6e-135  2.6e-135       2     362 ..      10     370 ..       9     371 .. 0.99

  Alignments for each domain:
  == domain 1  score: 437.2 bits;  conditional E-value: 2.6e-135
                                 TIGR01027   2 riVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQa 70 
                                               r VvK+Gs++Lt++ + l+r+ +a  v+q+ +l+++G e+v+vsSGavaaG+++Lg + rp  ++e Qa
  lcl|NCBI__GCF_900100495.1:WP_090439933.1  10 RWVVKIGSALLTADGRGLDRAAMAVWVRQMVALREQGVELVLVSSGAVAAGMSRLGWTARPSAMHELQA 78 
                                               67******************************************************************* PP

                                 TIGR01027  71 laaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvavee 139
                                               +aa+GQ  L++++e++f+++g+++aQiLLt++dls+r+rylNar+tl++l+el+vvp++NENDtv ++e
  lcl|NCBI__GCF_900100495.1:WP_090439933.1  79 AAAIGQMVLIQAWESSFAEHGRRTAQILLTHDDLSDRKRYLNARSTLRTLVELDVVPVINENDTVVTDE 147
                                               ********************************************************************* PP

                                 TIGR01027 140 ikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTG 208
                                               i+fGDNDtL+alva+lveAdlLv+ltd dg+y+adpr+np A+li e ++ + +l+avag+ g ++G G
  lcl|NCBI__GCF_900100495.1:WP_090439933.1 148 IRFGDNDTLAALVANLVEADLLVILTDRDGMYNADPRHNPGAELIYEARADDPALDAVAGGVGGALGRG 216
                                               ********************************************************************* PP

                                 TIGR01027 209 GmrtKleaaelAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkiiv 277
                                               Gm+tKl aa+lA+r+g +++i+ g+ ++ +a+l +++ +gtl++++++ l +rkqw++ +++++G++++
  lcl|NCBI__GCF_900100495.1:WP_090439933.1 217 GMQTKLRAARLAARSGAHTVIVGGAIEQVLARLRSGERLGTLLAPERSLLAARKQWLAGHLQTRGTLVL 285
                                               ********************************************************************* PP

                                 TIGR01027 278 degaeeallekgksLlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkseeiedv 346
                                               d+ga++al++ +ksLlp+gv +v+g+F+rge+v ++ ++g+ei++gl+nys+ e +ki g++se ie +
  lcl|NCBI__GCF_900100495.1:WP_090439933.1 286 DAGAVKALVSDRKSLLPVGVKAVQGSFRRGEMVVCVGPDGREIARGLANYSALEAQKIIGQSSEAIERL 354
                                               ********************************************************************* PP

                                 TIGR01027 347 Lgyekkeevvhrdnlv 362
                                               Lgy ++ e vhrdnl+
  lcl|NCBI__GCF_900100495.1:WP_090439933.1 355 LGYVDEPELVHRDNLI 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: 00:00:00.02
# Mc/sec: 6.74
//
[ok]

This GapMind analysis is from Apr 10 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