Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate GFF4352 HP15_p187g60 asparagine synthase, glutamine-hydrolyzing
Query= SwissProt::P64248 (652 letters) >FitnessBrowser__Marino:GFF4352 Length = 657 Score = 323 bits (829), Expect = 1e-92 Identities = 228/666 (34%), Positives = 334/666 (50%), Gaps = 54/666 (8%) Query: 1 MCGLLAFVAAPAGAAGPEGADAASAIARASHLMRHRGPDESGTWHAVDGASGGVVFGFNR 60 MCG+ G G E SA+ + + + HRGPD+SGTW + S G+ FG R Sbjct: 1 MCGITGIFG---GVPGSE--PLKSALKQMADAITHRGPDDSGTWEEL---SAGLGFGHRR 52 Query: 61 LSIIDIAHS-HQPLRWGPPEAPDRYVLVFNGEIYNYLELRDELRTQH--GAVFATDGDGE 117 LSI+D++ + HQP+ G R+VL FNGEIYN+ LR EL + A + D E Sbjct: 53 LSIVDLSPAGHQPMLSGC----GRFVLAFNGEIYNHNALRRELESSGKVSAGWKGHSDTE 108 Query: 118 AILAGYHHWGTE-VLQRLRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAVASE 176 +L + WG E L+ GMFA ALWD + L ARD FG KPL+ AG +SE Sbjct: 109 TLLCAFTAWGVEKTLEMAAGMFAIALWDREEQSLTLARDRFGEKPLYYGLVAGALVFSSE 168 Query: 177 KKCLLDLVELVGFDTEIDHRALQHYTVLQYVPEPETLHRGVRRLESGCFAR-----IRAD 231 K L G E++ L+ Y V E++ + V +L +GC + IR Sbjct: 169 LKALQRAPRWRG---EVEPSVLESYLRFGCVGGQESIFKDVFKLPAGCLLKVSLLDIRHG 225 Query: 232 QLAPVITRYFVPRFAASPIT---NDNDQARYDEITAVLEDSVAKHMRADVTVGAFLSGGI 288 ++ PV+ R++ P AA N+N D + L S+ + M ADV +GAFLSGG+ Sbjct: 226 EMPPVV-RWWSPVEAAGAALGGRNNNPDMALDNVEQALVASIRQQMAADVPLGAFLSGGV 284 Query: 289 DSTAIAALAIRHNPRLI-TFTTGFEREGFSEIDVAVASAEAIGARHIAKVVSADEFVAAL 347 DS+ I AL + + TF+ GF+ + E + A A A +G H ++ + + Sbjct: 285 DSSLIGALMQSQTSQKVRTFSVGFDDPRYDESEHAAAVAAYLGTEHTTLRATSKMALDLV 344 Query: 348 PEIVWYLDEPVADPALVPLFFVAREARKHVKVVLSGEGADELFGGYTIYR-EPLSLRPFD 406 P++ DEP AD + +P ++ R+HV V LSG+ DELFGGY Y P Sbjct: 345 PKLPELYDEPFADSSQLPTCLISALTRQHVTVALSGDAGDELFGGYNRYVWVPRVWSKLS 404 Query: 407 YLPKPLRRSMGKVSKPLPEGMRGKSLLHRGSLTLEERY---------YGNARSFSGAQLR 457 +P P+R+++G++ K +P R L+ G L RY Y A + + R Sbjct: 405 RMPLPMRQTLGRMLKLVPSS-RYDRLMCLGRKVLPSRYQIRTFGEKLYKLADVLACSSDR 463 Query: 458 EVLPGF-----------RPDWTHTDVTAPVYAESAGWDPVARMQHIDLFTWLRGDILVKA 506 + G R D+ + +Y AG+DPV M +D ++ D+LVK Sbjct: 464 ALYGGLASMNRHPEQLLRTDYRSGNPVEDLYPALAGFDPVEWMMLMDTLNFMVDDVLVKV 523 Query: 507 DKITMANSLELRVPFLDPEVFAVASRLPAGAKITRTTTKYALRRALEPIVPAHVLHRPKL 566 D+ +MA+SLE+R PFLDPEVF A +LP ++ K+ALR+ L VP ++ RPK+ Sbjct: 524 DRSSMASSLEVRAPFLDPEVFKAAWQLPLDMRVRNGEGKWALRQILYRHVPRELIERPKM 583 Query: 567 GFPVPIRHWLRAGELLEWAYATVGSSQAGHL--VDIAAVYRMLDEHRCGSSDHSRRLWTM 624 GF +P+ WLR G L EWA +G + +D AV+ M D H G ++++LW + Sbjct: 584 GFAIPLDDWLR-GPLREWAEDLLGVRWLSQIPALDAKAVHLMWDRHIQGQGHYAQQLWAV 642 Query: 625 LIFMLW 630 L W Sbjct: 643 LQLSAW 648 Lambda K H 0.323 0.138 0.428 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: 1138 Number of extensions: 61 Number of successful extensions: 8 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: 652 Length of database: 657 Length adjustment: 38 Effective length of query: 614 Effective length of database: 619 Effective search space: 380066 Effective search space used: 380066 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 54 (25.4 bits)
Align candidate GFF4352 HP15_p187g60 (asparagine synthase, glutamine-hydrolyzing)
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.21430.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-136 441.9 0.0 2.8e-136 441.5 0.0 1.2 1 lcl|FitnessBrowser__Marino:GFF4352 HP15_p187g60 asparagine synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF4352 HP15_p187g60 asparagine synthase, glutamine-hydrolyzing # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 441.5 0.0 2.8e-136 2.8e-136 1 517 [] 2 585 .. 2 585 .. 0.86 Alignments for each domain: == domain 1 score: 441.5 bits; conditional E-value: 2.8e-136 TIGR01536 1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek.evvi 73 Cgi+gi+ ++ ++a+k+m++++ hRGPD++g+w++ +++ ++ghrRL+i+dls + +QP+ + + v+ lcl|FitnessBrowser__Marino:GFF4352 2 CGITGIFGGVPGSEPLKSALKQMADAITHRGPDDSGTWEE-LSAGLGFGHRRLSIVDLSPAgHQPMLSGCgRFVL 75 *********998888779**********************.799***************998****99989**** PP TIGR01536 74 vfnGEIYNheeLreeleekGy...eFetksDtEViLaayeewg.eelverLeGmFAfalwdekkgelflaRDrlG 144 fnGEIYNh++Lr+ele G ++++sDtE +L+a+ +wg e+++e+ +GmFA+alwd++++ l laRDr+G lcl|FitnessBrowser__Marino:GFF4352 76 AFNGEIYNHNALRRELESSGKvsaGWKGHSDTETLLCAFTAWGvEKTLEMAAGMFAIALWDREEQSLTLARDRFG 150 *******************9633369************************************************* PP TIGR01536 145 ikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal.....dgeek 214 kPLYy+ +g+l+f+SE+Kal ++++ + e++ ++l ++l + v ++++fk+v++l+++ l d lcl|FitnessBrowser__Marino:GFF4352 151 EKPLYYGLVAGALVFSSELKALQRAPRWRGEVEPSVLESYLRFGCVGGQESIFKDVFKLPAGCLLkvsllD---- 221 ********************************************99****************999654441.... PP TIGR01536 215 lee........ywevekee......vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakke 275 +++ +w+ + + ++++ + + ++++++l +++++++ advp+g++lSGG+DSsl+ a+++ + lcl|FitnessBrowser__Marino:GFF4352 222 IRHgemppvvrWWSPVEAAgaalggRNNNPDMALDNVEQALVASIRQQMAADVPLGAFLSGGVDSSLIGALMQSQ 296 333455667779998888789999988999999****************************************** PP TIGR01536 276 aksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllskla 350 ++v+tFs+gf+ ++ +des++a++va++lgteh+++ +++ +l+ ++++ +ep+a++++ p+ l+s l+ lcl|FitnessBrowser__Marino:GFF4352 297 TSQKVRTFSVGFD-DPRYDESEHAAAVAAYLGTEHTTLRATSKMALDLVPKLPELYDEPFADSSQLPTCLISALT 370 *************.************************************************************* PP TIGR01536 351 rekgvkVvLsGeGaDElfgGYeyfreakae..eale...............lpeaselaekkl............ 396 r++ v+V+LsG+ +DElfgGY+++ ++ + + + lcl|FitnessBrowser__Marino:GFF4352 371 RQH-VTVALSGDAGDELFGGYNRYVWVPRVwsKLSRmplpmrqtlgrmlklV----------Pssrydrlmclgr 434 ***.********************9875431044445555555555554440..........0444445555555 PP TIGR01536 397 ..............................llqaklakeselkellkakleeelkekeelkkelkee........ 433 l+ + + + ++ll++++++++ + lcl|FitnessBrowser__Marino:GFF4352 435 kvlpsryqirtfgeklykladvlacssdraLYGGLASMNRHPEQLLRTDYRSGNPVE---------Dlypalagf 500 555665666666666665555555544442222233333334455555555544433.........144444556 PP TIGR01536 434 seleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPe 507 +e ++ d+ +++ d++++k Dr sma slEvR+PflD e++++a+++p ++++r+g+ K+ Lr+++ +++P+ lcl|FitnessBrowser__Marino:GFF4352 501 DPVEWMMLMDTLNFMVDDVLVKvDRSSMASSLEVRAPFLDPEVFKAAWQLPLDMRVRNGEGKWALRQILYRHVPR 575 899************************************************************************ PP TIGR01536 508 eileRkKeaf 517 e+ eR+K++f lcl|FitnessBrowser__Marino:GFF4352 576 ELIERPKMGF 585 ********99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (517 nodes) Target sequences: 1 (657 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 7.88 // [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