Align glutamine synthetase, type I (characterized)
to candidate WP_011735572.1 PPRO_RS08360 type I glutamate--ammonia ligase
Query= metacyc::SYNPCC7942_2156-MONOMER (473 letters) >NCBI__GCF_000015045.1:WP_011735572.1 Length = 470 Score = 629 bits (1621), Expect = 0.0 Identities = 297/469 (63%), Positives = 368/469 (78%), Gaps = 1/469 (0%) Query: 4 TAQEVLQLIQEKGIQLVDLKFIDMPGIWQHLTLHVSQIDENSFVEGVPFDGSSIRGWKAI 63 T ++V++ +E G +VD KF+D G WQH+++ +++ DE++F EG FDGSSIRGW+ I Sbjct: 2 TPKQVVEFAKENGALMVDYKFMDFVGTWQHVSVPITEFDEDTFEEGQGFDGSSIRGWQPI 61 Query: 64 NESDMTMVPDPTTAWIDPFMKEPTLSMICTIYEPRTNTPYERCPRAIAQKAVDYLKASGI 123 + SDM ++PDPT+A +DPF+ PTLS+IC I++P T Y R PR IA+KA YLK++G+ Sbjct: 62 HASDMILLPDPTSAKMDPFIAVPTLSLICDIFDPITKEDYTRDPRNIAKKAEMYLKSTGL 121 Query: 124 GDTAYFGPEAEFFIFDDVRFDQAENKSYYYVDSIEGRWNSGREEEGGNLGYKPRYKEGYF 183 GDTA+FGPEAEFFIFDDVRFD N+S+Y VDS EG WN+GREE NLGYKPR+KEGYF Sbjct: 122 GDTAFFGPEAEFFIFDDVRFDSGPNQSFYAVDSSEGAWNTGREEFP-NLGYKPRFKEGYF 180 Query: 184 PVAPTDTSQDMRSEMLLTMADCGVPIEKHHHEVATGGQCELGFRFGKLIEAADWLMTYKY 243 P +P D+ D+R+EM+ + + G+ +E HHEVATGGQ E+ RF L++ AD L +KY Sbjct: 181 PCSPVDSQNDLRNEMVQELQNVGIRVECQHHEVATGGQAEIDMRFSPLVDMADQLQWFKY 240 Query: 244 VIKNVGRRYGKTITFMPKPLFNDNGSGMHTHQSIWNDGQPLFAGDQYAGLSQMALWYIGG 303 VIKNV R KT+TFMPKPLF DNGSGMH H SIW DG LFAGD+Y GLSQMALWYIGG Sbjct: 241 VIKNVAYRNNKTVTFMPKPLFGDNGSGMHCHVSIWKDGVNLFAGDKYGGLSQMALWYIGG 300 Query: 304 ILKHAPALLALTNPTTNSYKRLVPGFEAPVNLAYSQGNRSASVRIPLSGTNPKAKRLEFR 363 I+KHA AL A+TNPTTNSYKRLVPGFEAPVN+AYS NRSA++RIP+ TNPKAKR+E+R Sbjct: 301 IIKHAKALCAITNPTTNSYKRLVPGFEAPVNIAYSSRNRSAAIRIPMMSTNPKAKRVEYR 360 Query: 364 CPDATSNPYLAFAAMLCAGIDGIKNQIDPGEPLDVDIYDLSPEELAKIPSTPGSLKDALK 423 PD + N YLAFAA+L AG+DGI+N+IDPG+PLD DIY LSPEEL IPS PGSL++AL Sbjct: 361 TPDPSCNGYLAFAALLMAGLDGIENKIDPGQPLDKDIYGLSPEELKSIPSAPGSLEEALN 420 Query: 424 ALEADHDFLTVGGVFTEDFIQNWIEYKLDNEVIPISLRPHPYEFALYYD 472 L+ DH+FL G VFT D I+ WIEYK+D EV PI +RP P EF+LYYD Sbjct: 421 CLKEDHEFLLKGDVFTPDVIEKWIEYKMDAEVNPIRMRPTPLEFSLYYD 469 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: 787 Number of extensions: 35 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: 470 Length adjustment: 33 Effective length of query: 440 Effective length of database: 437 Effective search space: 192280 Effective search space used: 192280 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_011735572.1 PPRO_RS08360 (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.19682.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-207 675.9 0.0 1.5e-207 675.7 0.0 1.0 1 lcl|NCBI__GCF_000015045.1:WP_011735572.1 PPRO_RS08360 type I glutamate--a Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015045.1:WP_011735572.1 PPRO_RS08360 type I glutamate--ammonia ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 675.7 0.0 1.5e-207 1.5e-207 2 462 .] 5 469 .. 4 469 .. 0.98 Alignments for each domain: == domain 1 score: 675.7 bits; conditional E-value: 1.5e-207 TIGR00653 2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 +v++++ke+ +vd +f+D G++++v++p++e++e+++eeg FDgss++G++ i+ sD++l pdp lcl|NCBI__GCF_000015045.1:WP_011735572.1 5 QVVEFAKENGALMVDYKFMDFVGTWQHVSVPITEFDEDTFEEGQGFDGSSIRGWQPIHASDMILLPDPT 73 78999**************************************************************** PP TIGR00653 71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138 +++++Pf+a ++l++icd+++p+tke y rdpR+iak+ae +lk t+lgd+++fGpEaEFf+fd+v+f+ lcl|NCBI__GCF_000015045.1:WP_011735572.1 74 SAKMDPFIAVPTLSLICDIFDPITKEDYTRDPRNIAKKAEMYLKsTGLGDTAFFGPEAEFFIFDDVRFD 142 ********************************************************************* PP TIGR00653 139 easnssflevdseegewn.reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHH 206 + n+sf++vds eg+wn ++e n gyk++ k+gYf+ pvD+++d+r+e+v++l+++g++ve +HH lcl|NCBI__GCF_000015045.1:WP_011735572.1 143 SGPNQSFYAVDSSEGAWNtGREEFPNLGYKPRFKEGYFPCSPVDSQNDLRNEMVQELQNVGIRVECQHH 211 ******************5455566******************************************** PP TIGR00653 207 Evata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgen 274 Evat+ qaEid++f+ lv++aD+++ +Kyv+knva ++ kt+tFmpKplfgdngsGmH+h+s+wkdg n lcl|NCBI__GCF_000015045.1:WP_011735572.1 212 EVATGgQAEIDMRFSPLVDMADQLQWFKYVIKNVAYRNNKTVTFMPKPLFGDNGSGMHCHVSIWKDGVN 280 ********************************************************************* PP TIGR00653 275 lfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPas 343 lfag++ y gLs++al+yigGi+kHakal A+tnpt+nsYkRLvpG+EAPv++ays +nRsa+iRiP++ lcl|NCBI__GCF_000015045.1:WP_011735572.1 281 LFAGDK-YGGLSQMALWYIGGIIKHAKALCAITNPTTNSYKRLVPGFEAPVNIAYSSRNRSAAIRIPMM 348 ******.*************************************************************9 PP TIGR00653 344 a.npkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesL 411 + npkakR+E+R+pDps+n YLafaallmAgldGi+nkidpg+pldk++y ls+eelk+ i++ p sL lcl|NCBI__GCF_000015045.1:WP_011735572.1 349 StNPKAKRVEYRTPDPSCNGYLAFAALLMAGLDGIENKIDPGQPLDKDIYGLSPEELKS--IPSAPGSL 415 99*********************************************************..******** PP TIGR00653 412 eealdelesdk..evlkevlgeelieafielkr.kEveelrlkvhpvElekyld 462 eeal+ l++d+ +++++v++ ++ie++ie+k+ +Ev+++r++++p+E++ y+d lcl|NCBI__GCF_000015045.1:WP_011735572.1 416 EEALNCLKEDHefLLKGDVFTPDVIEKWIEYKMdAEVNPIRMRPTPLEFSLYYD 469 ***********98899*****************99*****************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (462 nodes) Target sequences: 1 (470 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: 00:00:00.01 # Mc/sec: 10.87 // [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