GapMind for Amino acid biosynthesis

 

Aligments for a candidate for proB in Magnetospirillum magneticum AMB-1

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate WP_011386430.1 AMB_RS20630 glutamate 5-kinase

Query= BRENDA::P0A7B5
         (367 letters)



>lcl|NCBI__GCF_000009985.1:WP_011386430.1 AMB_RS20630 glutamate
           5-kinase
          Length = 370

 Score =  260 bits (664), Expect = 5e-74
 Identities = 153/367 (41%), Positives = 213/367 (58%), Gaps = 5/367 (1%)

Query: 1   MSDSQTLVVKLGTSVLTGGSR-RLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREH 59
           ++ ++ L+VK+G+S+L   S  ++ R  +  L    A   A G  +++V+SGA+A GR  
Sbjct: 4   LAAAKRLIVKIGSSLLVDDSTGQVRRGWLETLAADIAACKARGQEVIVVSSGAVAVGRRK 63

Query: 60  LGYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARD 119
           LG    P  +  KQ  AA GQ RL   W+   + + I V Q+LLT  D E+R R+LNAR 
Sbjct: 64  LGLVP-PLKLEEKQAAAATGQIRLAHAWQDALAHHQITVAQVLLTLDDSENRRRYLNARS 122

Query: 120 TLRALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADP 179
           TL  LL    VPVINEND VATAEI+VGDND L+A  A +  AD L+L +D  GLYTADP
Sbjct: 123 TLETLLKLGAVPVINENDTVATAEIRVGDNDRLAARVAQMVSADALVLFSDIDGLYTADP 182

Query: 180 RSNPQAELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKP 239
           R +P A  I +V+ +   + A+AGD  S  G+GGM TKL AA +   AG    I  G   
Sbjct: 183 RKDPDARFIPEVHELTPEIEAMAGDPGSAYGSGGMVTKLVAARICLSAGCRMAITRGEPM 242

Query: 240 GVIGDVMEGISVGTLFHAQATPLENRKRWIFGA-PPAGEITVDEGATAAILERGSSLLPK 298
             +  + +G    T F   + P   RK+WIFG+  P G + +D GA  A L +G SLLP 
Sbjct: 243 HPLKTIEDG-GRCTWFLPNSEPRTARKQWIFGSMKPTGTLVLDAGAARA-LAQGRSLLPA 300

Query: 299 GIKSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVA 358
           GI  V+G F RG+ + + +  G+ +  G+  Y++D  R I G  S EI+AILG+      
Sbjct: 301 GITEVSGAFERGDCVLVKDGSGKVLGRGLVAYSADDSRAIMGRKSGEIEAILGFRGRDEL 360

Query: 359 VHRDDMI 365
           +HRDD++
Sbjct: 361 IHRDDLV 367


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: 385
Number of extensions: 21
Number of successful extensions: 3
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: 370
Length adjustment: 30
Effective length of query: 337
Effective length of database: 340
Effective search space:   114580
Effective search space used:   114580
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_011386430.1 AMB_RS20630 (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.4220.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.8e-129  415.9   0.0   8.8e-129  415.7   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011386430.1  AMB_RS20630 glutamate 5-kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011386430.1  AMB_RS20630 glutamate 5-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.7   0.0  8.8e-129  8.8e-129       1     362 [.       8     367 ..       8     368 .. 0.98

  Alignments for each domain:
  == domain 1  score: 415.7 bits;  conditional E-value: 8.8e-129
                                 TIGR01027   1 kriVvKlGsssLteesgk.lkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaek 68 
                                               kr++vK+Gss+L+++s+  ++r  l++l++++a+ k+ G+ev++vsSGava+G ++Lgl   p kl+ek
  lcl|NCBI__GCF_000009985.1:WP_011386430.1   8 KRLIVKIGSSLLVDDSTGqVRRGWLETLAADIAACKARGQEVIVVSSGAVAVGRRKLGLVP-PLKLEEK 75 
                                               699***********99888***************************************975.99***** PP

                                 TIGR01027  69 QalaaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvav 137
                                               Qa+aa GQ rL +++++++++++++vaQ+LLt +d ++r+rylNar+tle+ll+lg+vp++NENDtva+
  lcl|NCBI__GCF_000009985.1:WP_011386430.1  76 QAAAATGQIRLAHAWQDALAHHQITVAQVLLTLDDSENRRRYLNARSTLETLLKLGAVPVINENDTVAT 144
                                               ********************************************************************* PP

                                 TIGR01027 138 eeikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvG 206
                                               +ei++GDND+L+a va++v+Ad+Lvl++d+dgLy+adpr++pdA++i+ev+e++ e++a+ag+ gs++G
  lcl|NCBI__GCF_000009985.1:WP_011386430.1 145 AEIRVGDNDRLAARVAQMVSADALVLFSDIDGLYTADPRKDPDARFIPEVHELTPEIEAMAGDPGSAYG 213
                                               ********************************************************************* PP

                                 TIGR01027 207 TGGmrtKleaaelAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGki 275
                                                GGm tKl aa++  +ag ++ i++ge p + ++ +ed    t f ++++   +rkqwi+  ++++G++
  lcl|NCBI__GCF_000009985.1:WP_011386430.1 214 SGGMVTKLVAARICLSAGCRMAITRGE-PMHPLKTIEDGGRCTWFLPNSEPRTARKQWIFGSMKPTGTL 281
                                               **************************9.6777788999999**************************** PP

                                 TIGR01027 276 ivdegaeeallekgksLlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkseeie 344
                                               ++d+ga++al + g+sLlpag++ev+g F+rg++v +++ +g+ +g+glv+ys+++ + i+g+ks eie
  lcl|NCBI__GCF_000009985.1:WP_011386430.1 282 VLDAGAARALAQ-GRSLLPAGITEVSGAFERGDCVLVKDGSGKVLGRGLVAYSADDSRAIMGRKSGEIE 349
                                               **********98.******************************************************** PP

                                 TIGR01027 345 dvLgyekkeevvhrdnlv 362
                                               ++Lg++ ++e +hrd+lv
  lcl|NCBI__GCF_000009985.1:WP_011386430.1 350 AILGFRGRDELIHRDDLV 367
                                               ****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (370 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: 00:00:00.02
# Mc/sec: 6.40
//
[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