GapMind for Amino acid biosynthesis

 

Aligments for a candidate for proB in Shewanella loihica PV-4

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate 5210407 Shew_2848 gamma-glutamyl kinase (RefSeq)

Query= BRENDA::P0A7B5
         (367 letters)



>lcl|FitnessBrowser__PV4:5210407 Shew_2848 gamma-glutamyl kinase
           (RefSeq)
          Length = 374

 Score =  445 bits (1145), Expect = e-130
 Identities = 226/360 (62%), Positives = 286/360 (79%), Gaps = 1/360 (0%)

Query: 7   LVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHLGYPELP 66
           +VVKLGTSVLT GSR+L++AH+VEL RQ A+L  +G  +V+ TSGAIAAGREHLGYP LP
Sbjct: 13  VVVKLGTSVLTSGSRQLDKAHMVELARQMAKLMKSGVEVVLCTSGAIAAGREHLGYPTLP 72

Query: 67  ATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDTLRALLD 126
            T+A+KQLLAAVGQS+LI  W QLFSIYG+HVGQ+LLTRAD+ DRER+LNARD+L ALL 
Sbjct: 73  DTVANKQLLAAVGQSQLILAWSQLFSIYGLHVGQLLLTRADLHDRERYLNARDSLNALLA 132

Query: 127 NNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPRSNPQAE 186
           N I+P+INENDAVAT EIKVGDNDNLSA AA+L  AD L+LLTDQKGL+ ADPR+NP A+
Sbjct: 133 NGIIPIINENDAVATNEIKVGDNDNLSARAALLCDADLLILLTDQKGLFDADPRANPDAK 192

Query: 187 LIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPGVIGDVM 246
           LIK V  IDD+LR++AG +VSGLGTGGM+TKLQAAD+A RAG++ +IA+G  P VI D +
Sbjct: 193 LIKQVVNIDDSLRSLAGGAVSGLGTGGMATKLQAADIARRAGVEVVIASGHHPKVILDAV 252

Query: 247 EGISVGTLFHAQATPLENRKRWIFGAPPA-GEITVDEGATAAILERGSSLLPKGIKSVTG 305
             + VGT F A   PLE+RK+WI   P   G + +D GA  A+  +G SLL KGI SV+G
Sbjct: 253 CQLPVGTHFTALENPLESRKQWILAGPATKGRLVLDSGAINAVTLKGRSLLSKGIVSVSG 312

Query: 306 NFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAVHRDDMI 365
            F RG  +++ + +GR+ A G+SRY++  L++IAG HS EI+++LGY+YG   VHR+DM+
Sbjct: 313 VFDRGATLQLVDEQGREHARGMSRYSAKDLQKIAGKHSDEIESLLGYDYGDAIVHRNDMV 372


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: 426
Number of extensions: 11
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: 374
Length adjustment: 30
Effective length of query: 337
Effective length of database: 344
Effective search space:   115928
Effective search space used:   115928
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 5210407 Shew_2848 (gamma-glutamyl kinase (RefSeq))
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.30496.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-146  473.8   1.4   2.2e-146  473.6   1.4    1.0  1  lcl|FitnessBrowser__PV4:5210407  Shew_2848 gamma-glutamyl kinase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210407  Shew_2848 gamma-glutamyl kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  473.6   1.4  2.2e-146  2.2e-146       1     363 []      11     373 ..      11     373 .. 1.00

  Alignments for each domain:
  == domain 1  score: 473.6 bits;  conditional E-value: 2.2e-146
                        TIGR01027   1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaaVGQgr 78 
                                      +r+VvKlG+s+Lt++s++l++++++el++q+akl+k G evv+ +SGa+aaG e+Lg+p+ p ++a+kQ+laaVGQ++
  lcl|FitnessBrowser__PV4:5210407  11 RRVVVKLGTSVLTSGSRQLDKAHMVELARQMAKLMKSGVEVVLCTSGAIAAGREHLGYPTLPDTVANKQLLAAVGQSQ 88 
                                      59**************************************************************************** PP

                        TIGR01027  79 LmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDtLsalvaalv 156
                                      L+ ++++lfs+ygl+v+Q+LLtradl++rerylNar++l++ll++g++pi+NEND+va++eik+GDND+Lsa  a l 
  lcl|FitnessBrowser__PV4:5210407  89 LILAWSQLFSIYGLHVGQLLLTRADLHDRERYLNARDSLNALLANGIIPIINENDAVATNEIKVGDNDNLSARAALLC 166
                                      ****************************************************************************** PP

                        TIGR01027 157 eAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaaelAsragveviiasgek 234
                                      +AdlL+lltd++gL+dadpr npdAkli++v +i+++l+++ag++ s +GTGGm+tKl+aa++A ragvev+iasg++
  lcl|FitnessBrowser__PV4:5210407 167 DADLLILLTDQKGLFDADPRANPDAKLIKQVVNIDDSLRSLAGGAVSGLGTGGMATKLQAADIARRAGVEVVIASGHH 244
                                      ****************************************************************************** PP

                        TIGR01027 235 pekiadlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekgksLlpagvvevegnFsrgevvei 312
                                      p+ i+d++ + +vgt f+a ++ l++rkqwila++++kG++++d+ga +a++ kg+sLl +g+v+v+g F+rg ++++
  lcl|FitnessBrowser__PV4:5210407 245 PKVILDAVCQLPVGTHFTALENPLESRKQWILAGPATKGRLVLDSGAINAVTLKGRSLLSKGIVSVSGVFDRGATLQL 322
                                      ****************************************************************************** PP

                        TIGR01027 313 laeegqeigkglvnysseelekikglkseeiedvLgyekkeevvhrdnlvl 363
                                      ++e+g+e ++g+++ys+++l+ki+g++s+eie +Lgy + + +vhr+++v+
  lcl|FitnessBrowser__PV4:5210407 323 VDEQGREHARGMSRYSAKDLQKIAGKHSDEIESLLGYDYGDAIVHRNDMVV 373
                                      ************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (374 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.95
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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:

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:

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:

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, or view the source code, or see 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