Alignments for a candidate for proB in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Bacteroides thetaiotaomicron VPI-5482

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate 353245 BT3719 glutamate 5-kinase (NCBI ptt file)

Query= reanno::Btheta:353245
         (360 letters)



>FitnessBrowser__Btheta:353245
          Length = 360

 Score =  703 bits (1814), Expect = 0.0
 Identities = 360/360 (100%), Positives = 360/360 (100%)

Query: 1   MKQEFTRIAVKVGSNVLARRDGTLDVTRMSALVDQIAELNKSGVEIILISSGAVASGRSE 60
           MKQEFTRIAVKVGSNVLARRDGTLDVTRMSALVDQIAELNKSGVEIILISSGAVASGRSE
Sbjct: 1   MKQEFTRIAVKVGSNVLARRDGTLDVTRMSALVDQIAELNKSGVEIILISSGAVASGRSE 60

Query: 61  IHPQKKLDSVDQRQLFSAVGQAKLINRYYELFREHGIAVGQVLTTKENFSTRRHYLNQKN 120
           IHPQKKLDSVDQRQLFSAVGQAKLINRYYELFREHGIAVGQVLTTKENFSTRRHYLNQKN
Sbjct: 61  IHPQKKLDSVDQRQLFSAVGQAKLINRYYELFREHGIAVGQVLTTKENFSTRRHYLNQKN 120

Query: 121 CMTVMLENGVIPIVNENDTISVSELMFTDNDELSGLIASMMDAQALIILSNIDGIYNGSP 180
           CMTVMLENGVIPIVNENDTISVSELMFTDNDELSGLIASMMDAQALIILSNIDGIYNGSP
Sbjct: 121 CMTVMLENGVIPIVNENDTISVSELMFTDNDELSGLIASMMDAQALIILSNIDGIYNGSP 180

Query: 181 SDPASAVIREIEHGKDLSNYIQATKSSFGRGGMLTKTNIARKVADEGITVIIANGKRDNI 240
           SDPASAVIREIEHGKDLSNYIQATKSSFGRGGMLTKTNIARKVADEGITVIIANGKRDNI
Sbjct: 181 SDPASAVIREIEHGKDLSNYIQATKSSFGRGGMLTKTNIARKVADEGITVIIANGKRDNI 240

Query: 241 LVDLLQQPDDTVCTRFIPSTEAVSSVKKWIAHSEGFAKGEIHINECATDILSSEKAASIL 300
           LVDLLQQPDDTVCTRFIPSTEAVSSVKKWIAHSEGFAKGEIHINECATDILSSEKAASIL
Sbjct: 241 LVDLLQQPDDTVCTRFIPSTEAVSSVKKWIAHSEGFAKGEIHINECATDILSSEKAASIL 300

Query: 301 PVGITHIEGEFEKDDIVRIMDFLGNQVGVGKANCDSAQAREAMGKHGKKPVVHYDYLYIE 360
           PVGITHIEGEFEKDDIVRIMDFLGNQVGVGKANCDSAQAREAMGKHGKKPVVHYDYLYIE
Sbjct: 301 PVGITHIEGEFEKDDIVRIMDFLGNQVGVGKANCDSAQAREAMGKHGKKPVVHYDYLYIE 360


Lambda     K      H
   0.316    0.133    0.369 

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: 578
Number of extensions: 5
Number of successful extensions: 1
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: 360
Length of database: 360
Length adjustment: 29
Effective length of query: 331
Effective length of database: 331
Effective search space:   109561
Effective search space used:   109561
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate 353245 BT3719 (glutamate 5-kinase (NCBI ptt file))
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.7142.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    1.9e-97  312.6   2.0    2.2e-97  312.4   2.0    1.0  1  lcl|FitnessBrowser__Btheta:353245  BT3719 glutamate 5-kinase (NCBI 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:353245  BT3719 glutamate 5-kinase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.4   2.0   2.2e-97   2.2e-97       2     341 ..       7     348 ..       6     358 .. 0.96

  Alignments for each domain:
  == domain 1  score: 312.4 bits;  conditional E-value: 2.2e-97
                          TIGR01027   2 riVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaaVGQg 77 
                                        ri vK+Gs++L++ +g+l+ +++++lv q+a+l+k G e++++sSGava+G +++  +++  ++ ++Q+ +aVGQ+
  lcl|FitnessBrowser__Btheta:353245   7 RIAVKVGSNVLARRDGTLDVTRMSALVDQIAELNKSGVEIILISSGAVASGRSEIHPQKKLDSVDQRQLFSAVGQA 82 
                                        899************************************************************************* PP

                          TIGR01027  78 rLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDtLsalva 153
                                        +L+++y +lf ++g+ v+Q+L t++++s+r++ylN +n ++ +le+gv+pivNENDt++v+e+ f DND+Ls l+a
  lcl|FitnessBrowser__Btheta:353245  83 KLINRYYELFREHGIAVGQVLTTKENFSTRRHYLNQKNCMTVMLENGVIPIVNENDTISVSELMFTDNDELSGLIA 158
                                        **************************************************************************** PP

                          TIGR01027 154 alveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaaelAsragvevii 229
                                        ++++A++L++l+++dg+y+  p ++p   +i e+e+ ++  ++++++  ss+G GGm tK + a+  ++ g+ vii
  lcl|FitnessBrowser__Btheta:353245 159 SMMDAQALIILSNIDGIYNGSP-SDPASAVIREIEHGKDLSNYIQATK-SSFGRGGMLTKTNIARKVADEGITVII 232
                                        **********************.9********************9885.77************************* PP

                          TIGR01027 230 asgekpekiadlle..daavgtlfeakkkklknrkqwilaase.akGkiivdegaeeallekgks.Llpagvveve 301
                                        a+g++ + ++dll+  d +v t f ++++ +++ k+wi++ +  akG+i ++e a++ l++++++ +lp+g++++e
  lcl|FitnessBrowser__Btheta:353245 233 ANGKRDNILVDLLQqpDDTVCTRFIPSTEAVSSVKKWIAHSEGfAKGEIHINECATDILSSEKAAsILPVGITHIE 308
                                        *************95568899******************9875389*************9765544********** PP

                          TIGR01027 302 gnFsrgevveilaeegqeigkglvnysseelekikglkse 341
                                        g+F++ ++v+i++  g+++g g++n +s++ ++ +g++ +
  lcl|FitnessBrowser__Btheta:353245 309 GEFEKDDIVRIMDFLGNQVGVGKANCDSAQAREAMGKHGK 348
                                        **********************************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (360 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.80
//
[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