Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate Pf6N2E2_2542 Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4)
Query= CharProtDB::CH_005185 (632 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2542 Length = 590 Score = 258 bits (659), Expect = 5e-73 Identities = 190/626 (30%), Positives = 294/626 (46%), Gaps = 56/626 (8%) Query: 1 MCGFVGV--FNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDV 58 MCG G F++ P A ++++ + RGPD+ G+ + G RRL I+D+ Sbjct: 1 MCGLAGELRFDQQPADLAA-----VERITHHLAPRGPDAWGFHSQGPIALGHRRLKIMDL 55 Query: 59 ENGG-QPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEA 117 +G QP+ + FNG IYNY ELR ELE GY+F + DTEVLL Y + E Sbjct: 56 SDGSAQPMIDNQLGLSLAFNGAIYNYPELRSELEGLGYSFYSGGDTEVLLKGYHAWGEAL 115 Query: 118 ASKLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQNDIE-- 175 KL GMFAF IW ++ L+ ARD G+KPLY + ++ FAS +L+ DI Sbjct: 116 LPKLNGMFAFAIWERDAKRLFIARDRLGVKPLYLSRTGQRLRFASALPALLKG-GDINPM 174 Query: 176 IDKEALQQYMSFQ-FVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANFKP----V 230 +D AL Y++F VP P TL A V+K+ P + I DG KT++ + P + Sbjct: 175 LDPVALNHYLNFHAVVPAPRTLLAGVEKMPPATWMRIEADGSTEQKTWWTLPYGPRADEL 234 Query: 231 QTEEDKLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFH-PSLKTFSVG 289 + ++ V D+ ++V + R+ V VG LSGG+DSS +V + +E L TFS+G Sbjct: 235 HLNLEDWIERVLDSTREAVAIRQRAAVDVGVLLSGGVDSSMLVGLLREVGVEDLSTFSIG 294 Query: 290 FEQQG---FSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLY 346 F+ G E + A G + I +E + +LP +P+ I Y Sbjct: 295 FQDAGGERGDEFQYSDLIAKHYGTRHHQLRIDEKEIIEQLPAAFRAMSEPMVSHDCIAFY 354 Query: 347 FVAKEAKKHVTVALSGEGADELFGGYNIYREPLSLKPFERIPSGLKKMLLHVAAVMPEGM 406 +++E KH V SG+GADELF GY+ Y + A P Sbjct: 355 LLSREVAKHCKVVQSGQGADELFAGYHWYPQV-------------------DGASDPYAA 395 Query: 407 RGKSLLERGCTPLQDRYIGNAKIFEESVKKQLLKHYNPNLSYRDVTKTYFTESSSYSDIN 466 + +R EE K N + D K +F + + + ++ Sbjct: 396 YRAAFFDRS--------------HEEYAATVQPKWLTANDAAGDFVKEHFAQPGADAAVD 441 Query: 467 KMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKNGTTKYL 526 K +D + D + + D MTMA LE R PFLD + ++++++P + K +G K + Sbjct: 442 KALRLDSTVMLVDDPVKRVDNMTMAWGLEARTPFLDYRLVELSARVPAKFKLPDG-GKQV 500 Query: 527 LRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQESQTDAYIHKDYVL-QLL 585 L++AA ++P V++RKK FPVP L+ WVR ++ + D + +L +LL Sbjct: 501 LKEAARRVIPGEVIDRKKGYFPVPGLKHLEGNTLAWVRELLLDPSQDRGLFNPAMLDRLL 560 Query: 586 EDHCADKAD-NSRKIWTVLIFMIWHS 610 D ++W + +W S Sbjct: 561 TDPNGQLTPLRGSRLWQLAALNLWLS 586 Lambda K H 0.319 0.136 0.403 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: 905 Number of extensions: 43 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 632 Length of database: 590 Length adjustment: 37 Effective length of query: 595 Effective length of database: 553 Effective search space: 329035 Effective search space used: 329035 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: 53 (25.0 bits)
Align candidate Pf6N2E2_2542 (Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4))
to HMM TIGR01536 (asnB: asparagine synthase (glutamine-hydrolyzing) (EC 6.3.5.4))
# 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/TIGR01536.hmm # target sequence database: /tmp/gapView.13497.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01536 [M=517] Accession: TIGR01536 Description: asn_synth_AEB: asparagine synthase (glutamine-hydrolyzing) 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-127 411.4 0.0 4.1e-127 411.2 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2542 Asparagine synthetase [glutamine Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2542 Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 411.2 0.0 4.1e-127 4.1e-127 1 516 [. 2 520 .. 2 521 .. 0.90 Alignments for each domain: == domain 1 score: 411.2 bits; conditional E-value: 4.1e-127 TIGR01536 1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQ 63 Cg+ag + +++ + + +a++++++ la RGPDa g++++ +lghrRL i+dls+g aQ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2542 2 CGLAGELRFDQQPA-DLAAVERITHHLAPRGPDAWGFHSQ---GPIALGHRRLKIMDLSDGsAQ 61 *******9988755.579******************6555...9******************** PP TIGR01536 64 Plsnek.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAf 126 P+ +++ + fnG IYN+ eLr ele Gy+F + DtEV+L+ y++wge+l+ +L+GmFAf lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2542 62 PMIDNQlGLSLAFNGAIYNYPELRSELEGLGYSFYSGGDTEVLLKGYHAWGEALLPKLNGMFAF 125 *******99******************************************************* PP TIGR01536 127 alwdekkgelflaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlq.l 189 a+w++ +++lf+aRDrlG+kPLY ++++++l faS + all+ +i+++ld al ++l ++ + lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2542 126 AIWERDAKRLFIARDRLGVKPLYLSRTGQRLRFASALPALLKGGDINPMLDPVALNHYLNFHaV 189 **************************************************************99 PP TIGR01536 190 vptektlfkevkelepakal....dgeekleeywevekee....vkeseeelveelrelledav 245 vp ++tl ++v++++pa + dg+++ +++w + + + ++e+ +e++ + ++av lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2542 190 VPAPRTLLAGVEKMPPATWMrieaDGSTEQKTWWTLPYGPradeLHLNLEDWIERVLDSTREAV 253 9****************999998888889999***9887745556778899************* PP TIGR01536 246 kkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsigfe..dskdldeskaarkvadelg 307 + r +a v vgvllSGG+DSs+++ ++++ +++ tFsigf+ + + de ++ +a++ g lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2542 254 AIRQRAAVDVGVLLSGGVDSSMLVGLLREVGVEDLSTFSIGFQdaGGERGDEFQYSDLIAKHYG 317 ******************************999*********965567788889********** PP TIGR01536 308 tehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvLsGeGaDElfgGY 371 t+h+++ i+e+e++++l+ ++a+ ep+ +++i ylls+++ ++ +kVv sG+GaDElf+GY lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2542 318 TRHHQLRIDEKEIIEQLPAAFRAMSEPMVSHDCIAFYLLSREVAKH-CKVVQSGQGADELFAGY 380 **********************************************.***************** PP TIGR01536 372 eyfreakaeealelpeaselaekklllqaklakeselke.llkakleeelkekeelkkelkees 434 +++ + + + a a+++ + +++ ++ ++ + + + +++ ++e++++ ++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2542 381 HWYPQVDGASDPY---A---AYRAAFFDRSHEEYAATVQpKWLTANDAAGDFVKEHFAQPGADA 438 ****975444443...2...23333333333333333220233334445556677788888889 PP TIGR01536 435 eleellrldlelllsdl.lrakDrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlL 497 +++++lrld + +l d+ +++ D ++ma++lE+R PflD +lvel +++p++ kl dg K +L lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2542 439 AVDKALRLDSTVMLVDDpVKRVDNMTMAWGLEARTPFLDYRLVELSARVPAKFKLPDG-GKQVL 501 99*****999988876626666**********************************98.799** PP TIGR01536 498 reaaeellPeeileRkKea 516 +eaa++++P e+ +RkK lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2542 502 KEAARRVIPGEVIDRKKGY 520 ****************965 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (517 nodes) Target sequences: 1 (590 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: 00:00:00.02 # Mc/sec: 14.03 // [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