Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate AO356_03575 AO356_03575 asparagine synthase
Query= CharProtDB::CH_005185 (632 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_03575 Length = 590 Score = 262 bits (670), Expect = 3e-74 Identities = 192/626 (30%), Positives = 295/626 (47%), 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 ELEA GYTF + DTEVLL Y + E Sbjct: 56 SDGSAQPMIDNQLGLSLAFNGAIYNYPELRTELEALGYTFYSGGDTEVLLKGYHAWGEAL 115 Query: 118 ASKLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQNDIE-- 175 KL GMFAF IW ++ L+ ARD G+KPLY + ++ FAS +L+ DI Sbjct: 116 LPKLNGMFAFAIWERDAKRLFIARDRLGVKPLYLSRTGQRLRFASALPALLKG-GDINPM 174 Query: 176 IDKEALQQYMSFQ-FVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANFKPVQTEE 234 +D AL Y++F VP P TL A V+K+ P + I DG KT++ + P E+ Sbjct: 175 LDPVALNHYLNFHAVVPAPRTLLAGVEKLPPATWMRIEADGTTEQKTWWTLPYGPRADEQ 234 Query: 235 ----DKLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFH-PSLKTFSVG 289 + + V D+ ++V + R+ V VG LSGG+DSS +V + +E L TFS+G Sbjct: 235 HLNLEDWIDRVLDSTREAVAIRQRAAVDVGVLLSGGVDSSMLVGLLREVGVEDLSTFSIG 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 N + D K +F + + + ++ Sbjct: 396 YRAAFFDRS--------------YEEYAATVQPNWLTANDAAGDFVKEHFAQPGADAAVD 441 Query: 467 KMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKNGTTKYL 526 K +D + D + + D MTMA LE R PFLD + ++++++P + K +G K + Sbjct: 442 KALRLDSTVMLVDDPVKRVDNMTMAWGLEARTPFLDYRLVELSARVPAQFKLPDG-GKQV 500 Query: 527 LRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQESQTDAYIHKDYVL-QLL 585 L++AA ++P V++RKK FPVP L+ WVR ++ + D + +L +LL Sbjct: 501 LKEAARRVIPSEVIDRKKGYFPVPGLKHLEGHTLAWVRELLLDPSQDRGLFNPAMLDRLL 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: 914 Number of extensions: 42 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 AO356_03575 AO356_03575 (asparagine synthase)
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.9966.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-128 415.9 0.0 1.7e-128 415.7 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03575 AO356_03575 asparagine synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03575 AO356_03575 asparagine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 415.7 0.0 1.7e-128 1.7e-128 1 516 [. 2 520 .. 2 521 .. 0.91 Alignments for each domain: == domain 1 score: 415.7 bits; conditional E-value: 1.7e-128 TIGR01536 1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.a 62 Cg+ag + +++ + + +a++++++ la RGPDa g++++ +lghrRL i+dls+g a lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03575 2 CGLAGELRFDQQPA-DLAAVERITHHLAPRGPDAWGFHSQ---GPIALGHRRLKIMDLSDGsA 60 *******9988755.579******************6555...9******************* PP TIGR01536 63 QPlsnek.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmF 124 QP+ +++ + fnG IYN+ eLr ele+ Gy+F + DtEV+L+ y++wge+l+ +L+GmF lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03575 61 QPMIDNQlGLSLAFNGAIYNYPELRTELEALGYTFYSGGDTEVLLKGYHAWGEALLPKLNGMF 123 ********99***************************************************** PP TIGR01536 125 AfalwdekkgelflaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltl 187 Afa+w++ +++lf+aRDrlG+kPLY ++++++l faS + all+ +i+++ld al ++l + lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03575 124 AFAIWERDAKRLFIARDRLGVKPLYLSRTGQRLRFASALPALLKGGDINPMLDPVALNHYLNF 186 *************************************************************** PP TIGR01536 188 q.lvptektlfkevkelepakal....dgeekleeywevekee....vkeseeelveelrell 241 + +vp ++tl ++v++l+pa + dg+++ +++w + + ++ ++e+ ++++ + lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03575 187 HaVVPAPRTLLAGVEKLPPATWMrieaDGTTEQKTWWTLPYGPradeQHLNLEDWIDRVLDST 249 *999****************999998888888888***9887655557778999********* PP TIGR01536 242 edavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsigfe..dskdldeskaarkv 302 ++av+ r +a v vgvllSGG+DSs+++ ++++ +++ tFsigf+ + + de ++ + lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03575 250 REAVAIRQRAAVDVGVLLSGGVDSSMLVGLLREVGVEDLSTFSIGFQdaGGERGDEFQYSDLI 312 **********************************999*********965567788889***** PP TIGR01536 303 adelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvLsGeGaD 365 a++ gt+h+++ i+e+e++++l+ ++a+ ep+ +++i ylls+++ ++ +kVv sG+GaD lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03575 313 AKHYGTRHHQLRIDEKEIIEQLPAAFRAMSEPMVSHDCIAFYLLSREVAKH-CKVVQSGQGAD 374 ***************************************************.*********** PP TIGR01536 366 ElfgGYeyfreakaeealelpeaselaekklllqaklakeselke.llkakleeelkekeelk 427 Elf+GY+++ + + + + a+++ + ++++++ ++ + + + +++ ++e++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03575 375 ELFAGYHWYPQVDGASDP---Y---AAYRAAFFDRSYEEYAATVQpNWLTANDAAGDFVKEHF 431 **********97444443...3...34455566666666555544134444455556677788 PP TIGR01536 428 kelkeeseleellrldlelllsdl.lrakDrvsmahslEvRvPflDkelvelalsippelklr 489 ++ ++ +++++lrld + +l d+ +++ D ++ma++lE+R PflD +lvel +++p++ kl lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03575 432 AQPGADAAVDKALRLDSTVMLVDDpVKRVDNMTMAWGLEARTPFLDYRLVELSARVPAQFKLP 494 8888889********99988877626666********************************** PP TIGR01536 490 dgkeKvlLreaaeellPeeileRkKea 516 dg K +L+eaa++++P+e+ +RkK lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03575 495 DG-GKQVLKEAARRVIPSEVIDRKKGY 520 98.799******************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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 12.10 // [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