Align glutamine synthetase, type I (characterized)
to candidate WP_015797717.1 AFER_RS01260 type I glutamate--ammonia ligase
Query= metacyc::SYNPCC7942_2156-MONOMER (473 letters) >NCBI__GCF_000023265.1:WP_015797717.1 Length = 475 Score = 595 bits (1535), Expect = e-175 Identities = 285/472 (60%), Positives = 355/472 (75%), Gaps = 1/472 (0%) Query: 2 PETAQEVLQLIQEKGIQLVDLKFIDMPGIWQHLTLHVSQIDENSFVEGVPFDGSSIRGWK 61 P EV+ + +E+G+++VDL+F D+PG QH ++ + Q+ E+SF EG FDGSSIRG+K Sbjct: 3 PRAPHEVIAMAEEQGVEMVDLRFCDLPGTMQHFSVPIRQLTEDSFEEGFGFDGSSIRGFK 62 Query: 62 AINESDMTMVPDPTTAWIDPFMKEPTLSMICTIYEPRTNTPYERCPRAIAQKAVDYLKAS 121 INESDM + PDP +A++DPF K TL + C IY+P T PY+R PR +A A ++L+AS Sbjct: 63 TINESDMILKPDPRSAYLDPFRKHRTLVLNCFIYDPVTGQPYDRDPRRVAAAAEEHLRAS 122 Query: 122 GIGDTAYFGPEAEFFIFDDVRFDQAENKSYYYVDSIEGRWNSGREEEGGNLGYKPRYKEG 181 GI DTAYFGPEAEFFIFDDVR+ Q E+ + Y VDSIEG WN+ R E+G NLG K +K G Sbjct: 123 GIADTAYFGPEAEFFIFDDVRYHQDEHSASYVVDSIEGAWNTDRNEQGSNLGGKIPFKRG 182 Query: 182 YFPVAPTDTSQDMRSEMLLTMADCGVPIEKHHHEVATGGQCELGFRFGKLIEAADWLMTY 241 YFPV P D QD+RSEM+LTM G+ IE HHEVAT GQ E+ R+ L+ AD LM Y Sbjct: 183 YFPVPPMDKFQDLRSEMVLTMQALGIEIEVQHHEVATAGQAEIDMRYDTLLAMADKLMLY 242 Query: 242 KYVIKNVGRRYGKTITFMPKPLFNDNGSGMHTHQSIWNDGQPLF-AGDQYAGLSQMALWY 300 KYV+K+V ++ G T TFMPKPLF DNGSGMHTHQS+W DG+PLF YA LS++AL Y Sbjct: 243 KYVVKSVAQQGGYTATFMPKPLFQDNGSGMHTHQSLWRDGEPLFYESGGYADLSELALHY 302 Query: 301 IGGILKHAPALLALTNPTTNSYKRLVPGFEAPVNLAYSQGNRSASVRIPLSGTNPKAKRL 360 IGGIL HAP++LA PTTNSYKRLVPG+EAPVNL +SQ NRSA+ RIP+ +PKAKR+ Sbjct: 303 IGGILAHAPSILAFAAPTTNSYKRLVPGYEAPVNLVFSQRNRSAACRIPMYSLSPKAKRV 362 Query: 361 EFRCPDATSNPYLAFAAMLCAGIDGIKNQIDPGEPLDVDIYDLSPEELAKIPSTPGSLKD 420 EFRCPDA +NPYLAF+AML AG+DGI+N+I+P P D D++DL P+E +P+ P SL+ Sbjct: 363 EFRCPDAMANPYLAFSAMLLAGLDGIRNKIEPAGPDDRDLFDLPPDEARALPTVPSSLEG 422 Query: 421 ALKALEADHDFLTVGGVFTEDFIQNWIEYKLDNEVIPISLRPHPYEFALYYD 472 +L ALEADHD+L GGVF++D I WI YK EV I LRPHPYEFALYYD Sbjct: 423 SLAALEADHDYLLEGGVFSQDLIDTWIAYKRAEEVDAIRLRPHPYEFALYYD 474 Lambda K H 0.319 0.138 0.428 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: 766 Number of extensions: 30 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: 473 Length of database: 475 Length adjustment: 33 Effective length of query: 440 Effective length of database: 442 Effective search space: 194480 Effective search space used: 194480 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 (21.7 bits) S2: 51 (24.3 bits)
Align candidate WP_015797717.1 AFER_RS01260 (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.4279.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-204 665.0 0.0 3.1e-204 664.8 0.0 1.0 1 lcl|NCBI__GCF_000023265.1:WP_015797717.1 AFER_RS01260 type I glutamate--a Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023265.1:WP_015797717.1 AFER_RS01260 type I glutamate--ammonia ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 664.8 0.0 3.1e-204 3.1e-204 2 462 .] 8 474 .. 7 474 .. 0.99 Alignments for each domain: == domain 1 score: 664.8 bits; conditional E-value: 3.1e-204 TIGR00653 2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 ev+++++e+ v++vdlrf+D+ G+++++++p+++l+e+ +eeg FDgss++Gfk+i+esD++lkpdp lcl|NCBI__GCF_000023265.1:WP_015797717.1 8 EVIAMAEEQGVEMVDLRFCDLPGTMQHFSVPIRQLTEDSFEEGFGFDGSSIRGFKTINESDMILKPDPR 76 688999*************************************************************** PP TIGR00653 71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138 ++ +Pfr++++l+++c +y+pvt++py+rdpR +a aee+l+ ++++d++yfGpEaEFf+fd+v+ + lcl|NCBI__GCF_000023265.1:WP_015797717.1 77 SAYLDPFRKHRTLVLNCFIYDPVTGQPYDRDPRRVAAAAEEHLRaSGIADTAYFGPEAEFFIFDDVRYH 145 ********************************************9************************ PP TIGR00653 139 easnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsH 205 + ++s+ + vds+eg+wn r+++++n g ki k+gYf+v+p+Dk +d+r+e+vl++++lg+e+ev+H lcl|NCBI__GCF_000023265.1:WP_015797717.1 146 QDEHSASYVVDSIEGAWNtdRNEQGSNLGGKIPFKRGYFPVPPMDKFQDLRSEMVLTMQALGIEIEVQH 214 ******************97777888******************************************* PP TIGR00653 206 HEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdge 273 HEvata qaEid+++d+l+ +aD+++lyKyvvk va++ G+tatFmpKplf+dngsGmH+h+slw+dge lcl|NCBI__GCF_000023265.1:WP_015797717.1 215 HEVATAgQAEIDMRYDTLLAMADKLMLYKYVVKSVAQQGGYTATFMPKPLFQDNGSGMHTHQSLWRDGE 283 ********************************************************************* PP TIGR00653 274 nlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPa 342 +lf+++ gya+Lse al+yigGil Ha+++ A+++pt+nsYkRLvpGyEAPv+l++s++nRsa+ RiP+ lcl|NCBI__GCF_000023265.1:WP_015797717.1 284 PLFYESGGYADLSELALHYIGGILAHAPSILAFAAPTTNSYKRLVPGYEAPVNLVFSQRNRSAACRIPM 352 ********************************************************************* PP TIGR00653 343 sa.npkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpes 410 ++ +pkakR+E+R+pD+ anpYLaf+a+l AgldGi+nki+p p d++l++l+++e++ ++++p+s lcl|NCBI__GCF_000023265.1:WP_015797717.1 353 YSlSPKAKRVEFRCPDAMANPYLAFSAMLLAGLDGIRNKIEPAGPDDRDLFDLPPDEARA--LPTVPSS 419 ************************************************************..******* PP TIGR00653 411 Leealdelesdk..evlkevlgeelieafielkr.kEveelrlkvhpvElekyld 462 Le +l +le+d+ +++++v++++li+++i++kr +Ev+ +rl++hp+E++ y+d lcl|NCBI__GCF_000023265.1:WP_015797717.1 420 LEGSLAALEADHdyLLEGGVFSQDLIDTWIAYKRaEEVDAIRLRPHPYEFALYYD 474 ***********988899*****************999****************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (462 nodes) Target sequences: 1 (475 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 7.55 // [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