Alignments for a candidate for glnA in Methanosarcina mazei Go1

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Methanosarcina mazei Go1

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_011032914.1 MM_RS05025 type I glutamate--ammonia ligase

Query= BRENDA::Q8PY99
         (447 letters)



>NCBI__GCF_000007065.1:WP_011032914.1
          Length = 447

 Score =  914 bits (2363), Expect = 0.0
 Identities = 447/447 (100%), Positives = 447/447 (100%)

Query: 1   MVQMKKCTTKEDVLEAVKERDVKFIRTQFTDTLGIIKSWAIPAEQLEEAFENGVMFDGSS 60
           MVQMKKCTTKEDVLEAVKERDVKFIRTQFTDTLGIIKSWAIPAEQLEEAFENGVMFDGSS
Sbjct: 1   MVQMKKCTTKEDVLEAVKERDVKFIRTQFTDTLGIIKSWAIPAEQLEEAFENGVMFDGSS 60

Query: 61  IQGFTRIEESDMKLALDPSTFRILPWRPATGAVARILGDVYLPDGNPFKGDPRYVLKTAI 120
           IQGFTRIEESDMKLALDPSTFRILPWRPATGAVARILGDVYLPDGNPFKGDPRYVLKTAI
Sbjct: 61  IQGFTRIEESDMKLALDPSTFRILPWRPATGAVARILGDVYLPDGNPFKGDPRYVLKTAI 120

Query: 121 KEAEKMGFSMNVGPELEFFLFKLDANGNPTTELTDQGGYFDFAPLDRAQDVRRDIDYALE 180
           KEAEKMGFSMNVGPELEFFLFKLDANGNPTTELTDQGGYFDFAPLDRAQDVRRDIDYALE
Sbjct: 121 KEAEKMGFSMNVGPELEFFLFKLDANGNPTTELTDQGGYFDFAPLDRAQDVRRDIDYALE 180

Query: 181 HMGFQIEASHHEVAPSQHEIDFRFGDVLCTADNVVTFKYVVKSIAYHKGYYASFMPKPLF 240
           HMGFQIEASHHEVAPSQHEIDFRFGDVLCTADNVVTFKYVVKSIAYHKGYYASFMPKPLF
Sbjct: 181 HMGFQIEASHHEVAPSQHEIDFRFGDVLCTADNVVTFKYVVKSIAYHKGYYASFMPKPLF 240

Query: 241 GVNGSGMHSNQSLFKDGKNVFYDPDTPTKLSQDAMYYIGGLLKHIREFTAVTNPVVNSYK 300
           GVNGSGMHSNQSLFKDGKNVFYDPDTPTKLSQDAMYYIGGLLKHIREFTAVTNPVVNSYK
Sbjct: 241 GVNGSGMHSNQSLFKDGKNVFYDPDTPTKLSQDAMYYIGGLLKHIREFTAVTNPVVNSYK 300

Query: 301 RLVPGYEAPVYISWSAQNRSSLIRIPATRGNGTRIELRCPDPACNPYLAFALMLRAGLEG 360
           RLVPGYEAPVYISWSAQNRSSLIRIPATRGNGTRIELRCPDPACNPYLAFALMLRAGLEG
Sbjct: 301 RLVPGYEAPVYISWSAQNRSSLIRIPATRGNGTRIELRCPDPACNPYLAFALMLRAGLEG 360

Query: 361 IKNKIDPGEPTNVNIFHLSDKEREERGIRSLPADLKEAIDEMKGSKFVKEALGEHVFSHY 420
           IKNKIDPGEPTNVNIFHLSDKEREERGIRSLPADLKEAIDEMKGSKFVKEALGEHVFSHY
Sbjct: 361 IKNKIDPGEPTNVNIFHLSDKEREERGIRSLPADLKEAIDEMKGSKFVKEALGEHVFSHY 420

Query: 421 LCAKEMEWDEYKAVVHPWELSRYLSML 447
           LCAKEMEWDEYKAVVHPWELSRYLSML
Sbjct: 421 LCAKEMEWDEYKAVVHPWELSRYLSML 447


Lambda     K      H
   0.320    0.137    0.414 

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: 889
Number of extensions: 23
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: 447
Length of database: 447
Length adjustment: 33
Effective length of query: 414
Effective length of database: 414
Effective search space:   171396
Effective search space used:   171396
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_011032914.1 MM_RS05025 (type I glutamate--ammonia ligase)
to HMM TIGR00653 (glnA: glutamine synthetase, type I (EC 6.3.1.2))

# 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/TIGR00653.hmm
# target sequence database:        /tmp/gapView.6592.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00653  [M=462]
Accession:   TIGR00653
Description: GlnA: glutamine synthetase, type I
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.5e-181  588.2   0.0   5.9e-179  581.5   0.0    2.0  1  lcl|NCBI__GCF_000007065.1:WP_011032914.1  MM_RS05025 type I glutamate--amm


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000007065.1:WP_011032914.1  MM_RS05025 type I glutamate--ammonia ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  581.5   0.0  5.9e-179  5.9e-179       1     461 [.      11     444 ..      11     445 .. 0.98

  Alignments for each domain:
  == domain 1  score: 581.5 bits;  conditional E-value: 5.9e-179
                                 TIGR00653   1 eevlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdp 69 
                                               e+vl+ +ke++vkf++ +f+D+ G++k+ +ip+++le ea+e+g++FDgss++Gf++ieesD+ l  dp
  lcl|NCBI__GCF_000007065.1:WP_011032914.1  11 EDVLEAVKERDVKFIRTQFTDTLGIIKSWAIPAEQLE-EAFENGVMFDGSSIQGFTRIEESDMKLALDP 78 
                                               578999******************************6.******************************* PP

                                 TIGR00653  70 etlvivPfraek..vlrvicdvyepvtkepyerdpRsiakraeeelktklgdevyfGpEaEFflfdkve 136
                                               +t+ i+P+r ++  v+r+ +dvy p +++p+++dpR+++k+a +e  +k+g ++++GpE EFflf+ + 
  lcl|NCBI__GCF_000007065.1:WP_011032914.1  79 STFRILPWRPATgaVARILGDVYLP-DGNPFKGDPRYVLKTAIKEA-EKMGFSMNVGPELEFFLFKLDA 145
                                               *********99888***********.*******************9.5*****************9988 PP

                                 TIGR00653 137 fkeasnssflevdseegewnreveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsH 205
                                                +                        n + +++++ggYfd +p+D+a+d+rr++ +ale++g+++e+sH
  lcl|NCBI__GCF_000007065.1:WP_011032914.1 146 NG------------------------NPTTELTDQGGYFDFAPLDRAQDVRRDIDYALEHMGFQIEASH 190
                                               77........................4578999************************************ PP

                                 TIGR00653 206 HEvataqaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgen 274
                                               HEva++q+Eid++f +++ +aD++v++Kyvvk +a ++G++a+FmpKplfg ngsGmH ++sl+kdg+n
  lcl|NCBI__GCF_000007065.1:WP_011032914.1 191 HEVAPSQHEIDFRFGDVLCTADNVVTFKYVVKSIAYHKGYYASFMPKPLFGVNGSGMHSNQSLFKDGKN 259
                                               ********************************************************************* PP

                                 TIGR00653 275 lfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPas 343
                                               +f+++++ + Ls+ a+yyigG+lkH + ++A+tnp vnsYkRLvpGyEAPvy+++sa+nRs+liRiPa+
  lcl|NCBI__GCF_000007065.1:WP_011032914.1 260 VFYDPDTPTKLSQDAMYYIGGLLKHIREFTAVTNPVVNSYKRLVPGYEAPVYISWSAQNRSSLIRIPAT 328
                                               *******888*********************************************************** PP

                                 TIGR00653 344 anpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLe 412
                                               + ++++RiE+R+pDp++npYLafa +l Agl+Giknkidpgep++ n+++ls +e++e Gi++lp++L+
  lcl|NCBI__GCF_000007065.1:WP_011032914.1 329 R-GNGTRIELRCPDPACNPYLAFALMLRAGLEGIKNKIDPGEPTNVNIFHLSDKEREERGIRSLPADLK 396
                                               *.******************************************************************* PP

                                 TIGR00653 413 ealdelesdkevlkevlgeelieafielkrkEveelrlkvhpvElekyl 461
                                               ea+de++   + +ke+lge+++ +++ +k+ E++e++  vhp+El++yl
  lcl|NCBI__GCF_000007065.1:WP_011032914.1 397 EAIDEMKGS-KFVKEALGEHVFSHYLCAKEMEWDEYKAVVHPWELSRYL 444
                                               *******99.9*************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (447 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: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 3.30
//
[ok]

This GapMind analysis is from Apr 10 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