Alignments for a candidate for proB in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Cupriavidus basilensis 4G11

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate RR42_RS17940 RR42_RS17940 gamma-glutamyl kinase

Query= BRENDA::P0A7B5
         (367 letters)



>FitnessBrowser__Cup4G11:RR42_RS17940
          Length = 372

 Score =  285 bits (730), Expect = 1e-81
 Identities = 156/366 (42%), Positives = 219/366 (59%), Gaps = 1/366 (0%)

Query: 1   MSDSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHL 60
           ++ ++ +VVK+G+S++T   + L+   I     Q A+L  AG  +V+V+SGAIA G + L
Sbjct: 5   IAQAKRIVVKVGSSLVTNDGKGLDHEAIARWAAQIAKLRMAGKEVVLVSSGAIAEGMQRL 64

Query: 61  GYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDT 120
           G+   P  I   Q  AAVGQ  L Q++E  F  YGI   Q+LLT AD+ DRER+LNAR T
Sbjct: 65  GWVRRPKEIHELQAAAAVGQMGLAQVYESQFGRYGIRTAQVLLTHADLADRERYLNARST 124

Query: 121 LRALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPR 180
           L  LL   +VP+INEND V T EIK GDND L AL   L   D L++LTDQ+GLYTADPR
Sbjct: 125 LLTLLSLGVVPIINENDTVVTDEIKFGDNDTLGALVTNLIEGDALVILTDQRGLYTADPR 184

Query: 181 SNPQAELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPG 240
           SNPQAE + +       L A+AG + + +G GGM TK+ AA  A ++G  T+IA+G +  
Sbjct: 185 SNPQAEFVDEALAGAVELEAMAGGAGTSIGRGGMLTKILAAKRAAKSGAHTVIASGREAN 244

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

Query: 300 IKSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAV 359
           +  V G F+RGEVI   +  G ++A G++ Y S   + IA   S EI+ +LG++     +
Sbjct: 305 VVEVQGEFARGEVIACIDAAGHEVARGITNYASSEAKLIARKPSSEIERVLGHQNEHELI 364

Query: 360 HRDDMI 365
           HRD+++
Sbjct: 365 HRDNLV 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: 360
Number of extensions: 19
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 RR42_RS17940 RR42_RS17940 (gamma-glutamyl 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.5889.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.4e-135  435.3   3.9   1.1e-134  435.2   3.9    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS17940  RR42_RS17940 gamma-glutamyl kina


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS17940  RR42_RS17940 gamma-glutamyl kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.2   3.9  1.1e-134  1.1e-134       1     362 [.       9     370 ..       9     371 .. 0.99

  Alignments for each domain:
  == domain 1  score: 435.2 bits;  conditional E-value: 1.1e-134
                                 TIGR01027   1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQ 69 
                                               kriVvK+Gss++t++ + l+++ +a+ ++q+akl+ aG+evv+vsSGa+a G+++Lg  +rpk+++e Q
  lcl|FitnessBrowser__Cup4G11:RR42_RS17940   9 KRIVVKVGSSLVTNDGKGLDHEAIARWAAQIAKLRMAGKEVVLVSSGAIAEGMQRLGWVRRPKEIHELQ 77 
                                               69*************999*************************************************** PP

                                 TIGR01027  70 alaaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvave 138
                                               a+aaVGQ  L + ye++f +yg+++aQ+LLt+adl++rerylNar+tl +ll+lgvvpi+NENDtv ++
  lcl|FitnessBrowser__Cup4G11:RR42_RS17940  78 AAAAVGQMGLAQVYESQFGRYGIRTAQVLLTHADLADRERYLNARSTLLTLLSLGVVPIINENDTVVTD 146
                                               ********************************************************************* PP

                                 TIGR01027 139 eikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGT 207
                                               eikfGDNDtL alv++l+e d+Lv+ltd+ gLy+adpr+np+A++++e  + + el+a+ag++g+s+G 
  lcl|FitnessBrowser__Cup4G11:RR42_RS17940 147 EIKFGDNDTLGALVTNLIEGDALVILTDQRGLYTADPRSNPQAEFVDEALAGAVELEAMAGGAGTSIGR 215
                                               ********************************************************************* PP

                                 TIGR01027 208 GGmrtKleaaelAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkii 276
                                               GGm tK+ aa+ A+++g +++iasg++ + + +l+ ++ +gt++ a + +l +rkqw++ +++ +G+++
  lcl|FitnessBrowser__Cup4G11:RR42_RS17940 216 GGMLTKILAAKRAAKSGAHTVIASGREANVLERLAGGEGIGTQLLAPTGRLTARKQWMADHLQLRGRVV 284
                                               ********************************************************************* PP

                                 TIGR01027 277 vdegaeeallekgksLlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkseeied 345
                                               +d+ga+++l++ gksLlp gvvev+g+F rgev+ + + +g+e+++g +ny s+e + i++++s+eie 
  lcl|FitnessBrowser__Cup4G11:RR42_RS17940 285 IDAGAADKLTSGGKSLLPIGVVEVQGEFARGEVIACIDAAGHEVARGITNYASSEAKLIARKPSSEIER 353
                                               ********************************************************************* PP

                                 TIGR01027 346 vLgyekkeevvhrdnlv 362
                                               vLg+++++e +hrdnlv
  lcl|FitnessBrowser__Cup4G11:RR42_RS17940 354 VLGHQNEHELIHRDNLV 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.81
//
[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