Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase III; GSIII; EC 6.3.1.2 (characterized)
to candidate WP_106712819.1 CU102_RS19800 type III glutamate--ammonia ligase
Query= SwissProt::O87393 (435 letters) >NCBI__GCF_003010955.1:WP_106712819.1 Length = 435 Score = 802 bits (2071), Expect = 0.0 Identities = 379/435 (87%), Positives = 403/435 (92%) Query: 1 MTLDLSTFAREKGVKYFMISYTDLFGGQRAKLVPAEAIADMQKGGAGFAGFATWFDLTPA 60 MTLDLSTFA E GVKYFMISYTDL GGQRAKLVPA+AIADMQ+ GAGFAGFATW DLTPA Sbjct: 1 MTLDLSTFAAENGVKYFMISYTDLCGGQRAKLVPAQAIADMQRDGAGFAGFATWLDLTPA 60 Query: 61 HPDLFALPDASAVIQLPWKKDVAWVAADCIMDDAPVEQAPRVVLKKLVAEAAQEGLRVKT 120 HPDLFA+PDA +VIQLPWK+DVAWVAADC+M+DAPV+QAPRV+LK+LV EA Q+GLRVKT Sbjct: 61 HPDLFAVPDAGSVIQLPWKRDVAWVAADCMMEDAPVQQAPRVLLKRLVGEARQQGLRVKT 120 Query: 121 GVEPEFFLISPDGSKISDTFDTAEKPCYDQQAIMRRYDVIAEICDYMLELGWKPYQNDHE 180 GVEPEFFL++PDGS+ISD D+ EKPCYDQQA+MRRYDVIAEICD MLELGWKPYQNDHE Sbjct: 121 GVEPEFFLVTPDGSQISDQRDSGEKPCYDQQAVMRRYDVIAEICDCMLELGWKPYQNDHE 180 Query: 181 DANGQFEMNWEYDDALRTADKHSFFKFMVKSIAEKHGLRATFMPKPFKGLTGNGCHCHIS 240 DANGQFEMNWEYDDAL TADKHSFFKFMVKSIAEKHGLRATFMPKPFKGLTGNGCHCHIS Sbjct: 181 DANGQFEMNWEYDDALNTADKHSFFKFMVKSIAEKHGLRATFMPKPFKGLTGNGCHCHIS 240 Query: 241 VWDLAGEVNAFADNKAEFGLSAEGRHFLGGIMKHASALAAVTNPTVNSYKRINAPRTISG 300 VWD+ G NAFAD + FGLS G+ FLGGIMKHASALAAVTNPTVNSYKRINAPRT+SG Sbjct: 241 VWDVEGRTNAFADKRMPFGLSENGKTFLGGIMKHASALAAVTNPTVNSYKRINAPRTVSG 300 Query: 301 ATWAPNSVTWTGNNRTHMVRVPGPGRFELRLPDGAVNPYLLQAIIIAAGLSGVRSKADPG 360 ATWAPNSVTWTGNNRTHMVRVPGPGRFELRLPDGAVNPYLLQAIIIAAGLSG+R+ ADPG Sbjct: 301 ATWAPNSVTWTGNNRTHMVRVPGPGRFELRLPDGAVNPYLLQAIIIAAGLSGLRTNADPG 360 Query: 361 RHYDIDMYKDGHKVTDAPKLPLNLLDALREYNRDEELQEALGREFSAAYLKLKQGEWNTY 420 RHYDIDMYKDGH VTDAPKLPLNLLDALR Y DEELQ ALG EFS+AYLKLK EWN Y Sbjct: 361 RHYDIDMYKDGHTVTDAPKLPLNLLDALRAYESDEELQVALGTEFSSAYLKLKHSEWNAY 420 Query: 421 CSQFTEWEHQTTLDV 435 CSQFTEWEHQTTLD+ Sbjct: 421 CSQFTEWEHQTTLDI 435 Lambda K H 0.319 0.135 0.421 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: 788 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: 435 Length of database: 435 Length adjustment: 32 Effective length of query: 403 Effective length of database: 403 Effective search space: 162409 Effective search space used: 162409 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_106712819.1 CU102_RS19800 (type III glutamate--ammonia ligase)
to HMM TIGR03105 (glnT: glutamine synthetase, type III (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/TIGR03105.hmm # target sequence database: /tmp/gapView.2550268.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03105 [M=435] Accession: TIGR03105 Description: gln_synth_III: glutamine synthetase, type III 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-205 666.9 0.0 5.6e-205 666.8 0.0 1.0 1 NCBI__GCF_003010955.1:WP_106712819.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010955.1:WP_106712819.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 666.8 0.0 5.6e-205 5.6e-205 2 435 .] 6 434 .. 5 434 .. 0.99 Alignments for each domain: == domain 1 score: 666.8 bits; conditional E-value: 5.6e-205 TIGR03105 2 kklleekgvkyvlaafvdllGvakaklvPvealdalakegagfaGfavsglglePadadllavpdldsliqlP 74 +++++e+gvky++++++dl G ++aklvP++a+++++++gagfaGfa++ l+l+Pa++dl+avpd+ s+iqlP NCBI__GCF_003010955.1:WP_106712819.1 6 STFAAENGVKYFMISYTDLCGGQRAKLVPAQAIADMQRDGAGFAGFATW-LDLTPAHPDLFAVPDAGSVIQLP 77 67899********************************************.*********************** PP TIGR03105 75 wkpevawvaadlvvegkpvelapRvvlkkllaeaaekgftlktGveceffllrreedgklsvaDkaDklakpc 147 wk++vawvaad+++e++pv++apRv+lk+l+ ea ++g+++ktGve+effl++ + +++++D++D+ +kpc NCBI__GCF_003010955.1:WP_106712819.1 78 WKRDVAWVAADCMMEDAPVQQAPRVLLKRLVGEARQQGLRVKTGVEPEFFLVTPD---GSQISDQRDSGEKPC 147 ******************************************************9...899************ PP TIGR03105 148 YDqralmrrydvleeisealnelGwdlYqiDheDanGqfelnfeyaDalttaDrvaffkylvkeiaeeeglla 220 YDq+a+mrrydv++ei++++ elGw++Yq+DheDanGqfe+n+ey+Dal taD+++ffk++vk+iae++gl+a NCBI__GCF_003010955.1:WP_106712819.1 148 YDQQAVMRRYDVIAEICDCMLELGWKPYQNDHEDANGQFEMNWEYDDALNTADKHSFFKFMVKSIAEKHGLRA 220 ************************************************************************* PP TIGR03105 221 tfmPkPfadrtGnGlhlhlslldedg.knlfaddadeeglglsklayhfiaGilkhakaLaallaPtvnsYkR 292 tfmPkPf+ +tGnG+h+h+s++d +g +n+fad+ ++ +gls+ +++f++Gi+kha+aLaa+++PtvnsYkR NCBI__GCF_003010955.1:WP_106712819.1 221 TFMPKPFKGLTGNGCHCHISVWDVEGrTNAFADK--RMPFGLSENGKTFLGGIMKHASALAAVTNPTVNSYKR 291 *************************989*****9..9************************************ PP TIGR03105 293 lvakrtlsgatWaPalisyggnnRthmvRiPdagRlelRlaDgaanpYlvsaavlaaGLdGierkldpgkrkd 365 ++a+rt+sgatWaP+ ++++gnnRthmvR+P++gR+elRl+Dga+npYl++a+++aaGL G++ ++dpg+++d NCBI__GCF_003010955.1:WP_106712819.1 292 INAPRTVSGATWAPNSVTWTGNNRTHMVRVPGPGRFELRLPDGAVNPYLLQAIIIAAGLSGLRTNADPGRHYD 364 ************************************************************************* PP TIGR03105 366 enlyaeelaekgvetLPqtLlealraleadelleealGkelveeflklkreeweeyhrtvsdWeidryle 435 +++y+++++++++ +LP +Ll+alra+e+de l+ alG+e+++++lklk++ew++y++++++We +++l+ NCBI__GCF_003010955.1:WP_106712819.1 365 IDMYKDGHTVTDAPKLPLNLLDALRAYESDEELQVALGTEFSSAYLKLKHSEWNAYCSQFTEWEHQTTLD 434 ******************************************************************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (435 nodes) Target sequences: 1 (435 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 18.98 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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