Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_011024100.1 MA_RS22015 type I glutamate--ammonia ligase
Query= BRENDA::Q8PY99 (447 letters) >NCBI__GCF_000007345.1:WP_011024100.1 Length = 447 Score = 852 bits (2200), Expect = 0.0 Identities = 408/447 (91%), Positives = 429/447 (95%) Query: 1 MVQMKKCTTKEDVLEAVKERDVKFIRTQFTDTLGIIKSWAIPAEQLEEAFENGVMFDGSS 60 MVQMKKCTTKEDVLEAVKERDVKFIRTQFTDTLGIIKSWAIPAEQLEEAFENGVMFDGSS Sbjct: 1 MVQMKKCTTKEDVLEAVKERDVKFIRTQFTDTLGIIKSWAIPAEQLEEAFENGVMFDGSS 60 Query: 61 IQGFTRIEESDMKLALDPSTFRILPWRPATGAVARILGDVYLPDGNPFKGDPRYVLKTAI 120 IQGFTRIEESDMKL LDPSTFRILPWRPATGAVARILGDVYLPDG PF+GDPRYVLKTAI Sbjct: 61 IQGFTRIEESDMKLVLDPSTFRILPWRPATGAVARILGDVYLPDGKPFQGDPRYVLKTAI 120 Query: 121 KEAEKMGFSMNVGPELEFFLFKLDANGNPTTELTDQGGYFDFAPLDRAQDVRRDIDYALE 180 EAEKMGFSMNVGPELEFFLFKLDANGNPTTELTDQGGYFDFAPLDRAQDVRRDIDYALE Sbjct: 121 SEAEKMGFSMNVGPELEFFLFKLDANGNPTTELTDQGGYFDFAPLDRAQDVRRDIDYALE 180 Query: 181 HMGFQIEASHHEVAPSQHEIDFRFGDVLCTADNVVTFKYVVKSIAYHKGYYASFMPKPLF 240 HMGFQIEASHHEVAPSQHEIDFRF DVL TADNVVTFKYVVKSIAYHKGYYA+FMPKPLF Sbjct: 181 HMGFQIEASHHEVAPSQHEIDFRFSDVLNTADNVVTFKYVVKSIAYHKGYYATFMPKPLF 240 Query: 241 GVNGSGMHSNQSLFKDGKNVFYDPDTPTKLSQDAMYYIGGLLKHIREFTAVTNPVVNSYK 300 G NGSGMHSNQSLFK+GKN FYDPDTP +LSQDAMYYIGGL+ HI+EFTA+TNPV+NSYK Sbjct: 241 GENGSGMHSNQSLFKNGKNAFYDPDTPMQLSQDAMYYIGGLMSHIKEFTAITNPVINSYK 300 Query: 301 RLVPGYEAPVYISWSAQNRSSLIRIPATRGNGTRIELRCPDPACNPYLAFALMLRAGLEG 360 RLVPGYEAP+YI+WS++NRSSLIRIPATRG GTR+ELRCPDP+CNPYLAFALMLRAGL+G Sbjct: 301 RLVPGYEAPIYITWSSKNRSSLIRIPATRGEGTRVELRCPDPSCNPYLAFALMLRAGLDG 360 Query: 361 IKNKIDPGEPTNVNIFHLSDKEREERGIRSLPADLKEAIDEMKGSKFVKEALGEHVFSHY 420 IK+KIDPGE TNVNIFHL++KER ER I SLP DLKEAIDEMKGS+FVKE LGEHVFSHY Sbjct: 361 IKSKIDPGEATNVNIFHLTEKERAERSIHSLPGDLKEAIDEMKGSQFVKEVLGEHVFSHY 420 Query: 421 LCAKEMEWDEYKAVVHPWELSRYLSML 447 LCAKEMEWDEYKA+VHPWEL +YL ML Sbjct: 421 LCAKEMEWDEYKAIVHPWELEKYLPML 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: 833 Number of extensions: 27 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_011024100.1 MA_RS22015 (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.3713.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-180 586.3 0.0 2.2e-178 579.6 0.0 2.0 1 lcl|NCBI__GCF_000007345.1:WP_011024100.1 MA_RS22015 type I glutamate--amm Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000007345.1:WP_011024100.1 MA_RS22015 type I glutamate--ammonia ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 579.6 0.0 2.2e-178 2.2e-178 1 461 [. 11 444 .. 11 445 .. 0.98 Alignments for each domain: == domain 1 score: 579.6 bits; conditional E-value: 2.2e-178 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_000007345.1:WP_011024100.1 11 EDVLEAVKERDVKFIRTQFTDTLGIIKSWAIPAEQLE-EAFENGVMFDGSSIQGFTRIEESDMKLVLDP 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_000007345.1:WP_011024100.1 79 STFRILPWRPATgaVARILGDVYLP-DGKPFQGDPRYVLKTAISEA-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_000007345.1:WP_011024100.1 146 NG------------------------NPTTELTDQGGYFDFAPLDRAQDVRRDIDYALEHMGFQIEASH 190 77........................4578999************************************ PP TIGR00653 206 HEvataqaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgen 274 HEva++q+Eid++f++++++aD++v++Kyvvk +a ++G++atFmpKplfg+ngsGmH ++sl+k+g+n lcl|NCBI__GCF_000007345.1:WP_011024100.1 191 HEVAPSQHEIDFRFSDVLNTADNVVTFKYVVKSIAYHKGYYATFMPKPLFGENGSGMHSNQSLFKNGKN 259 ********************************************************************* PP TIGR00653 275 lfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPas 343 +f+++++ ++Ls+ a+yyigG+++H k ++A+tnp +nsYkRLvpGyEAP+y+++s knRs+liRiPa+ lcl|NCBI__GCF_000007345.1:WP_011024100.1 260 AFYDPDTPMQLSQDAMYYIGGLMSHIKEFTAITNPVINSYKRLVPGYEAPIYITWSSKNRSSLIRIPAT 328 *******888*********************************************************** PP TIGR00653 344 anpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLe 412 + ++++R+E+R+pDps+npYLafa +l AgldGik kidpge+++ n+++l+e+e++e i++lp +L+ lcl|NCBI__GCF_000007345.1:WP_011024100.1 329 R-GEGTRVELRCPDPSCNPYLAFALMLRAGLDGIKSKIDPGEATNVNIFHLTEKERAERSIHSLPGDLK 396 *.******************************************************************* PP TIGR00653 413 ealdelesdkevlkevlgeelieafielkrkEveelrlkvhpvElekyl 461 ea+de++ + +kevlge+++ +++ +k+ E++e++ vhp+Elekyl lcl|NCBI__GCF_000007345.1:WP_011024100.1 397 EAIDEMKGS-QFVKEVLGEHVFSHYLCAKEMEWDEYKAIVHPWELEKYL 444 *******99.9*************************************7 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: 3.09 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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:
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:
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