Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase III; GSIII (uncharacterized)
to candidate Synpcc7942_2296 Synpcc7942_2296 L-glutamine synthetase
Query= curated2:P31592 (435 letters) >FitnessBrowser__SynE:Synpcc7942_2296 Length = 434 Score = 539 bits (1388), Expect = e-158 Identities = 256/430 (59%), Positives = 320/430 (74%) Query: 5 LAAFARDKSIKYFMISYTDLFGGQRAKLVPAEAIADMQKDGAGFAGFATWLDLTPAHPDL 64 LAA ARD+ I+YF+I++TDLFG QRAKLVPA +I M GAGFAGFA WLDL+PA D+ Sbjct: 4 LAALARDRGIRYFLIAFTDLFGVQRAKLVPASSIDLMATSGAGFAGFAAWLDLSPADADV 63 Query: 65 FAVPDASSVIQLPWKKDVAWVAADCVMDDRPVEQAPRVVLKRLVAEAAKEGLRVKTGVEP 124 A+PD S+ QLPW+ +VAW+ AD ++D+P+EQAPR VLKR+++ A G R KTGVE Sbjct: 64 LAIPDRDSLFQLPWQPEVAWMPADLYLNDQPLEQAPRWVLKRVLSVAESLGYRPKTGVEC 123 Query: 125 EFFLISADGSVISDQFDTAEKPCYDQQAVMRRYDVIAEICDYMLELGWKPYQNDHEDANG 184 EFFL+ G I+D D KPCYDQQ++MRRYD+I +I + M ELGW PYQ+DHEDANG Sbjct: 124 EFFLLDETGDAIADPRDRQAKPCYDQQSLMRRYDLITQISEAMEELGWGPYQSDHEDANG 183 Query: 185 QFEMNWEYDDVLKTADKHSFFKFMVKSVAEKHGLRATFMPKPFKGLTGNGCHAHISVWDV 244 QFEMNW Y D L TAD+ +FFK+MVK++AE+ GLRATFMPKPF LTGNGCH H+S+W+ Sbjct: 184 QFEMNWTYADALVTADRQAFFKYMVKTLAERQGLRATFMPKPFADLTGNGCHMHLSLWNR 243 Query: 245 DGRVNAFADKEMAFGLSAQGKTFLGGIMKHAPALAAITNPTVNSYKRINAPRTTSGATWS 304 +G N F D LS G F+GG++ A +L A+TNPT+NSYKRINAP TTSGATWS Sbjct: 244 EGTTNTFVDPVATAPLSTLGYQFIGGLLHSAASLCALTNPTINSYKRINAPATTSGATWS 303 Query: 305 PNTVTWTGNNRTHMVRVPGPGRFELRLPDGAVNPYLLQAIIIAAGLEGIRSQADPGQHYD 364 PN ++++GNNRTH++R+P GRFELRL DGA NPYLL A IAAGL+GI+++ DPG YD Sbjct: 304 PNGISYSGNNRTHLIRIPDAGRFELRLADGAANPYLLPAAAIAAGLDGIQNKRDPGPRYD 363 Query: 365 IDMYAEGHLVKDAPRLPLNLLDALRAFDADEGLKAAIGAEFSSAYLKLKHLEWNAYCSHF 424 D YA+ P LP +LLDALR+ L +GA F+SAYLKLKH EW ++C+ Sbjct: 364 NDNYAQPLPPGTVPTLPEHLLDALRSLQESTVLTEGLGAAFTSAYLKLKHQEWRSFCAEI 423 Query: 425 TQWERDSTLD 434 T WER +TLD Sbjct: 424 TPWERATTLD 433 Lambda K H 0.320 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: 631 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: 434 Length adjustment: 32 Effective length of query: 403 Effective length of database: 402 Effective search space: 162006 Effective search space used: 162006 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 Synpcc7942_2296 Synpcc7942_2296 (L-glutamine synthetase)
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.13998.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.6e-212 689.4 0.0 8.6e-212 689.2 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_2296 Synpcc7942_2296 L-glutamine synt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_2296 Synpcc7942_2296 L-glutamine synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 689.2 0.0 8.6e-212 8.6e-212 2 435 .] 5 433 .. 4 433 .. 0.99 Alignments for each domain: == domain 1 score: 689.2 bits; conditional E-value: 8.6e-212 TIGR03105 2 kklleekgvkyvlaafvdllGvakaklvPvealdalakegagfaGfavsglglePadadllavpdldsl 70 ++l++++g++y+l+af+dl+Gv++aklvP++++d +a++gagfaGfa++ l+l+Padad+la+pd dsl lcl|FitnessBrowser__SynE:Synpcc7942_2296 5 AALARDRGIRYFLIAFTDLFGVQRAKLVPASSIDLMATSGAGFAGFAAW-LDLSPADADVLAIPDRDSL 72 6899*********************************************.******************* PP TIGR03105 71 iqlPwkpevawvaadlvvegkpvelapRvvlkkllaeaaekgftlktGveceffllrreedgklsvaDk 139 +qlPw+pevaw++adl+++++p+e+apR+vlk++l+ a++ g++ ktGveceffll+++ + ++aD lcl|FitnessBrowser__SynE:Synpcc7942_2296 73 FQLPWQPEVAWMPADLYLNDQPLEQAPRWVLKRVLSVAESLGYRPKTGVECEFFLLDET---GDAIADP 138 **********************************************************9...778**** PP TIGR03105 140 aDklakpcYDqralmrrydvleeisealnelGwdlYqiDheDanGqfelnfeyaDalttaDrvaffkyl 208 +D++akpcYDq++lmrryd++++isea++elGw++Yq+DheDanGqfe+n++yaDal+taDr+affky+ lcl|FitnessBrowser__SynE:Synpcc7942_2296 139 RDRQAKPCYDQQSLMRRYDLITQISEAMEELGWGPYQSDHEDANGQFEMNWTYADALVTADRQAFFKYM 207 ********************************************************************* PP TIGR03105 209 vkeiaeeegllatfmPkPfadrtGnGlhlhlslldedg.knlfaddadeeglglsklayhfiaGilkha 276 vk++ae++gl+atfmPkPfad+tGnG+h+hlsl++++g +n+f d+ ++ +ls+l+y+fi+G+l++a lcl|FitnessBrowser__SynE:Synpcc7942_2296 208 VKTLAERQGLRATFMPKPFADLTGNGCHMHLSLWNREGtTNTFVDP--VATAPLSTLGYQFIGGLLHSA 274 ***********************************99989******..999****************** PP TIGR03105 277 kaLaallaPtvnsYkRlvakrtlsgatWaPalisyggnnRthmvRiPdagRlelRlaDgaanpYlvsaa 345 ++L+al++Pt+nsYkR++a++t+sgatW+P+ isy+gnnRth++RiPdagR+elRlaDgaanpYl+ aa lcl|FitnessBrowser__SynE:Synpcc7942_2296 275 ASLCALTNPTINSYKRINAPATTSGATWSPNGISYSGNNRTHLIRIPDAGRFELRLADGAANPYLLPAA 343 ********************************************************************* PP TIGR03105 346 vlaaGLdGierkldpgkrkdenlyaeelaekgvetLPqtLlealraleadelleealGkelveeflklk 414 ++aaGLdGi++k+dpg+r+d+++ya++l +v tLP++Ll+alr+l+++++l+e lG+++++++lklk lcl|FitnessBrowser__SynE:Synpcc7942_2296 344 AIAAGLDGIQNKRDPGPRYDNDNYAQPLPPGTVPTLPEHLLDALRSLQESTVLTEGLGAAFTSAYLKLK 412 ********************************************************************* PP TIGR03105 415 reeweeyhrtvsdWeidryle 435 ++ew+++++++++We+ ++l+ lcl|FitnessBrowser__SynE:Synpcc7942_2296 413 HQEWRSFCAEITPWERATTLD 433 ****************99975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (435 nodes) Target sequences: 1 (434 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.12 // [ok]
This GapMind analysis is from Apr 09 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