Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha (uncharacterized)
to candidate WP_018232996.1 THITHI_RS0110215 type III glutamate--ammonia ligase
Query= curated2:O27612 (442 letters) >NCBI__GCF_000378965.1:WP_018232996.1 Length = 444 Score = 306 bits (784), Expect = 9e-88 Identities = 169/440 (38%), Positives = 263/440 (59%), Gaps = 27/440 (6%) Query: 17 VKFVRLQFVDIHGKPKNMAIPLVRPDQIEDIIKDGLLFDGSSVEGF-VDINESDLVLKPD 75 VK++ QFVDIHG K ++P+ +ED++ DG F G +V G + +E+D + + D Sbjct: 15 VKYILAQFVDIHGVAKTKSVPV---SHLEDVLTDGAGFAGFAVWGLRMGPHEADYMARGD 71 Query: 76 PDTFSTLPWRPEEKGVCRFICDIYWPDGKPFEGDPRYVLKRALDKYAHLGYEYNVGPEPE 135 T S +PW+P G R +CD + +G+P+ D R +L + + G+ N G EPE Sbjct: 72 LGTLSIVPWQP---GYARIVCDGF-VNGEPYMMDTRNILAAQVKRLKERGWTMNTGLEPE 127 Query: 136 FFILDQDEDGNIIPHDCG-----AYFDVEPVDQGTDFRRKLVMDLEALNFDVEVSHHEVA 190 F +L +D +G ++P D +D + + + +F +LV L+A++FDV HE A Sbjct: 128 FSLLRRDGNGGVVPADDSDRLDKPCYDYKGLSRSREFLERLVESLQAVDFDVYQVDHEDA 187 Query: 191 PGQHEIDFKFDKALKTADAVITFKQAIKAIVDKIGYMVTFMPKPFFGENGSGMHCHQSLF 250 GQ EI++ + + +AD + F+ A I +++G + +FMPKPF G+GMH H S+ Sbjct: 188 NGQFEINYTYSDCMTSADRYVFFRMAAGEIANQLGLICSFMPKPFSNRTGNGMHMHISIA 247 Query: 251 KD-GENVFYDPDTET--QLSEEALYFIGGLLKHAPALTAVCAPTVNSYKRLVPGYE---- 303 + N+F +P LS+ A +F+ GL++HAPALTA+ AP+VNSYKRLV G Sbjct: 248 DETNPNIFEEPSDPRGLSLSKTAYHFMAGLMEHAPALTALMAPSVNSYKRLVVGRALSGA 307 Query: 304 --APVYIAYGLKNRSTLIRIPASRGKGTRVELRMPDPSCNPYLAFAAMLEAGMNGIQNKI 361 AP +I+YG NR++++R+P R +ELR+ D +CNPYLA AA++ AG++G+ K+ Sbjct: 308 TWAPAFISYGDNNRTSMVRVPQGR-----LELRLGDGACNPYLAAAAVIAAGLDGVDRKL 362 Query: 362 DPGEPTEIDVYEKSMSELREMGIETLPSSLWEAYHALEEDDVIKGALGGHVYEKFMEIKH 421 +PGEP + Y+ S +EL E GIETLP SL EA L +D + LG ++F+E+K+ Sbjct: 363 EPGEPQNFNFYDFSPTELAEKGIETLPQSLHEAIETLRKDTLFAEQLGQAFIDEFVELKN 422 Query: 422 REWDDYRVRVFKYELERYLD 441 EW +Y V +EL RY++ Sbjct: 423 MEWVEYSRHVSDWELSRYVE 442 Lambda K H 0.320 0.141 0.433 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: 532 Number of extensions: 32 Number of successful extensions: 7 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: 442 Length of database: 444 Length adjustment: 32 Effective length of query: 410 Effective length of database: 412 Effective search space: 168920 Effective search space used: 168920 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_018232996.1 THITHI_RS0110215 (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.23362.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-202 657.6 0.0 3.9e-202 657.4 0.0 1.0 1 lcl|NCBI__GCF_000378965.1:WP_018232996.1 THITHI_RS0110215 type III glutam Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000378965.1:WP_018232996.1 THITHI_RS0110215 type III glutamate--ammonia ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 657.4 0.0 3.9e-202 3.9e-202 2 434 .. 7 441 .. 6 442 .. 0.99 Alignments for each domain: == domain 1 score: 657.4 bits; conditional E-value: 3.9e-202 TIGR03105 2 kklleekgvkyvlaafvdllGvakaklvPvealdalakegagfaGfavsglglePadadllavpdldsl 70 k+ le ++vky+la+fvd++Gvak+k+vPv++l++++++gagfaGfav+gl + P++ad++a +dl +l lcl|NCBI__GCF_000378965.1:WP_018232996.1 7 KTYLESHDVKYILAQFVDIHGVAKTKSVPVSHLEDVLTDGAGFAGFAVWGLRMGPHEADYMARGDLGTL 75 577999*************************************************************** PP TIGR03105 71 iqlPwkpevawvaadlvvegkpvelapRvvlkkllaeaaekgftlktGveceffllrreedgklsvaDk 139 +Pw+p++a++++d++v+g+p+ +++R++l +++++++e+g+t++tG+e+ef+llrr+ +g++++aD+ lcl|NCBI__GCF_000378965.1:WP_018232996.1 76 SIVPWQPGYARIVCDGFVNGEPYMMDTRNILAAQVKRLKERGWTMNTGLEPEFSLLRRDGNGGVVPADD 144 ********************************************************************* PP TIGR03105 140 aDklakpcYDqralmrrydvleeisealnelGwdlYqiDheDanGqfelnfeyaDalttaDrvaffkyl 208 +D+l+kpcYD+++l+r++++le+++e+l+++ +d+Yq+DheDanGqfe+n++y+D +t+aDr++ff+++ lcl|NCBI__GCF_000378965.1:WP_018232996.1 145 SDRLDKPCYDYKGLSRSREFLERLVESLQAVDFDVYQVDHEDANGQFEINYTYSDCMTSADRYVFFRMA 213 ********************************************************************* PP TIGR03105 209 vkeiaeeegllatfmPkPfadrtGnGlhlhlslldedgknlfaddadeeglglsklayhfiaGilkhak 277 + eia++ gl+++fmPkPf++rtGnG+h+h+s++de+ n+f++++d++gl lsk+ayhf+aG+++ha+ lcl|NCBI__GCF_000378965.1:WP_018232996.1 214 AGEIANQLGLICSFMPKPFSNRTGNGMHMHISIADETNPNIFEEPSDPRGLSLSKTAYHFMAGLMEHAP 282 ********************************************************************* PP TIGR03105 278 aLaallaPtvnsYkRlvakrtlsgatWaPalisyggnnRthmvRiPdagRlelRlaDgaanpYlvsaav 346 aL+al+aP+vnsYkRlv++r+lsgatWaPa+isyg+nnRt mvR+P +gRlelRl+Dga+npYl++aav lcl|NCBI__GCF_000378965.1:WP_018232996.1 283 ALTALMAPSVNSYKRLVVGRALSGATWAPAFISYGDNNRTSMVRVP-QGRLELRLGDGACNPYLAAAAV 350 **********************************************.9********************* PP TIGR03105 347 laaGLdGierkldpgkrkdenlya...eelaekgvetLPqtLlealraleadelleealGkelveeflk 412 +aaGLdG++rkl+pg++++ n+y+ elaekg+etLPq+L+ea+++l +d+l++e+lG+++++ef++ lcl|NCBI__GCF_000378965.1:WP_018232996.1 351 IAAGLDGVDRKLEPGEPQNFNFYDfspTELAEKGIETLPQSLHEAIETLRKDTLFAEQLGQAFIDEFVE 419 ************************9999***************************************** PP TIGR03105 413 lkreeweeyhrtvsdWeidryl 434 lk++ew+ey+r+vsdWe+ ry+ lcl|NCBI__GCF_000378965.1:WP_018232996.1 420 LKNMEWVEYSRHVSDWELSRYV 441 ********************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (435 nodes) Target sequences: 1 (444 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: 10.31 // [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