Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_106710730.1 CU102_RS08860 type I glutamate--ammonia ligase
Query= BRENDA::P0A1P6 (469 letters) >NCBI__GCF_003010955.1:WP_106710730.1 Length = 469 Score = 621 bits (1602), Expect = 0.0 Identities = 298/468 (63%), Positives = 370/468 (79%), Gaps = 1/468 (0%) Query: 2 SAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKGI 61 +A+ +L + +++VKF+DLRFTD KGK QHVT+ +V+ + F +G MFDGSSI GWK I Sbjct: 3 TAKDILKQIKDNDVKFLDLRFTDPKGKLQHVTMDVAEVDEDMFADGVMFDGSSIAGWKAI 62 Query: 62 NESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRATGI 121 NESDMVLMPD T +DPFFA ST++I CDIL+P + + Y+RDPR AK+AE Y++A GI Sbjct: 63 NESDMVLMPDTDTVHMDPFFAQSTMVILCDILDPISGEAYNRDPRGTAKKAEAYMKAEGI 122 Query: 122 ADTVLFGPEPEFFLFDDIRFGASISGSHVAIDDIEGAWNSSTKYEGGNKGHRPGVKGGYF 181 DT+ GPE EFF+FDD+++ A + +D E N T YE GN GHRP VKGGYF Sbjct: 123 GDTIFVGPEAEFFVFDDVKYKADPYNTGFKLDSTELPSNDDTDYETGNLGHRPRVKGGYF 182 Query: 182 PVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYKY 241 PVPPVDSAQD+RSEM V+ +MG+ VE HHHEVA A Q+E+ +F+ +T+ AD++ IYKY Sbjct: 183 PVPPVDSAQDMRSEMLTVLTEMGVRVEKHHHEVAAA-QHELGIKFDALTRNADKMLIYKY 241 Query: 242 VVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLAKNGTNLFSGDKYAGLSEQALYYIGG 301 VVH VA+ +GKTATFMPKP+FGDNGSGMH HMS+ K G F+G++YAGLSE L++IGG Sbjct: 242 VVHQVANAYGKTATFMPKPIFGDNGSGMHVHMSIWKEGKPTFAGNEYAGLSENCLFFIGG 301 Query: 302 VIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVASPKARRIEVRF 361 +IKHAKAINA NP+TNSYKRLVPGYEAPV+LAYSARNRSAS RIP +SPK++R+E+RF Sbjct: 302 IIKHAKAINAFTNPSTNSYKRLVPGYEAPVLLAYSARNRSASCRIPFGSSPKSKRVEIRF 361 Query: 362 PDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALNA 421 PDP ANPYL FAA+LMAGLDGIKNKIHPG+ MDK+LYDLP +E K+IP V GSL EAL + Sbjct: 362 PDPTANPYLGFAAMLMAGLDGIKNKIHPGQPMDKDLYDLPAKELKKIPTVCGSLREALQS 421 Query: 422 LDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV 469 LD DR FLKAGGVF D+ ID++I L+ E R MTPHPVE+++YYSV Sbjct: 422 LDKDRGFLKAGGVFDDDQIDSFIELKMAEVMRFEMTPHPVEYDMYYSV 469 Lambda K H 0.318 0.136 0.401 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: 753 Number of extensions: 25 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: 469 Length of database: 469 Length adjustment: 33 Effective length of query: 436 Effective length of database: 436 Effective search space: 190096 Effective search space used: 190096 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
Align candidate WP_106710730.1 CU102_RS08860 (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.3367942.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-203 662.6 0.0 1.7e-203 662.4 0.0 1.0 1 NCBI__GCF_003010955.1:WP_106710730.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010955.1:WP_106710730.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 662.4 0.0 1.7e-203 1.7e-203 2 462 .] 6 468 .. 5 468 .. 0.99 Alignments for each domain: == domain 1 score: 662.4 bits; conditional E-value: 1.7e-203 TIGR00653 2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpetlvi 74 ++lk +k+++vkf+dlrf+D kGkl++v++ v e++e+++ +g++FDgss+ G+k+i+esD++l+pd++t+ + NCBI__GCF_003010955.1:WP_106710730.1 6 DILKQIKDNDVKFLDLRFTDPKGKLQHVTMDVAEVDEDMFADGVMFDGSSIAGWKAINESDMVLMPDTDTVHM 78 68899******************************************************************** PP TIGR00653 75 vPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefkeasnssfl 146 +Pf a++++++ cd+ +p+ +e y+rdpR +ak+ae ++k +++gd++++GpEaEFf+fd+v+ k ++ + NCBI__GCF_003010955.1:WP_106710730.1 79 DPFFAQSTMVILCDILDPISGEAYNRDPRGTAKKAEAYMKaEGIGDTIFVGPEAEFFVFDDVKYKADPYNTGF 151 ************************************************************************* PP TIGR00653 147 evdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvataqaEidi 217 ++ds+e n +++e+gn g++++ kggYf+v+pvD+a+d+r+e++++l+e+g++ve++HHEva aq+E++i NCBI__GCF_003010955.1:WP_106710730.1 152 KLDSTELPSNddTDYETGNLGHRPRVKGGYFPVPPVDSAQDMRSEMLTVLTEMGVRVEKHHHEVAAAQHELGI 224 ******988878999********************************************************** PP TIGR00653 218 kfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetal 290 kfd l+++aD++++yKyvv++va+ +GktatFmpKp+fgdngsGmHvh+s+wk+g++ fag+e yagLse++l NCBI__GCF_003010955.1:WP_106710730.1 225 KFDALTRNADKMLIYKYVVHQVANAYGKTATFMPKPIFGDNGSGMHVHMSIWKEGKPTFAGNE-YAGLSENCL 296 ***************************************************************.********* PP TIGR00653 291 yyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanpY 363 ++igGi+kHaka++A+tnp++nsYkRLvpGyEAPv laysa+nRsa+ RiP ++pk+kR+E+R+pDp+anpY NCBI__GCF_003010955.1:WP_106710730.1 297 FFIGGIIKHAKAINAFTNPSTNSYKRLVPGYEAPVLLAYSARNRSASCRIPFGSSPKSKRVEIRFPDPTANPY 369 ************************************************************************* PP TIGR00653 364 LafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLeealdelesdk..evlkevlgeeli 434 L faa+lmAgldGiknki+pg+p+dk+ly+l+ +elk+ i+++ sL+eal++l++d+ +++++v+ ++ i NCBI__GCF_003010955.1:WP_106710730.1 370 LGFAAMLMAGLDGIKNKIHPGQPMDKDLYDLPAKELKK--IPTVCGSLREALQSLDKDRgfLKAGGVFDDDQI 440 **************************************..*******************9999********** PP TIGR00653 435 eafielkrkEveelrlkvhpvElekyld 462 ++fielk++Ev ++++++hpvE +y++ NCBI__GCF_003010955.1:WP_106710730.1 441 DSFIELKMAEVMRFEMTPHPVEYDMYYS 468 **************************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (462 nodes) Target sequences: 1 (469 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: 13.97 // [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