Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate WP_012976121.1 AZL_RS19060 asparagine synthase (glutamine-hydrolyzing)
Query= SwissProt::P64248 (652 letters) >NCBI__GCF_000010725.1:WP_012976121.1 Length = 684 Score = 218 bits (555), Expect = 7e-61 Identities = 179/596 (30%), Positives = 270/596 (45%), Gaps = 50/596 (8%) Query: 1 MCGLLAFVAAPAGAAGPEGADAASAIARASHLMRHRGPDESGTWHAVDGASGGVVFGFNR 60 MCG+ +A A P G D + R ++ HRGPD G + + R Sbjct: 1 MCGVAGVLAG--SRAEPAGLDE---LKRMIAMLSHRGPDGYGFYR-----DDRIGLAHAR 50 Query: 61 LSIIDIAHSHQPLRWGPPEAPDRYVLV-FNGEIYNYLELRDELRTQHGAVFATDGDGEAI 119 LSI+ +A QP+ DR + + FNGEI+N++ELR +L + G F T D E I Sbjct: 51 LSIVGLAGGFQPIH-----NEDRSLWISFNGEIFNHVELRRDLEAR-GHRFYTRTDTEVI 104 Query: 120 LAGYHHWGTEVLQRLRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAVASEKKC 179 + + +G RL G FA LWD REL+ RD GI PLF A ASE K Sbjct: 105 VHAFEEYGPATWARLNGQFAICLWDATRRELWLVRDRLGILPLFYARRGDHLVFASEAKA 164 Query: 180 LLDLVELVGFDTEIDH-RALQHYTVLQYVPEPETLHRGVRRLESGCFARIRADQLAPVIT 238 L + DH R Q +T P R V + + R+ + LA + Sbjct: 165 LFGGGRVA---PAFDHARLAQVFTHWSAAPHGSVFER-VESVPAATAIRVDS-TLALHVD 219 Query: 239 RYFVPRFAASP-ITNDNDQARYDEITAVLEDSVAKHMRADVTVGAFLSGGIDSTAIAALA 297 RY+ P F A P + + D + L D++ +RADV VG ++SGG+DS+ IAALA Sbjct: 220 RYWQPDFTADPALAKLSLDEAADRLEEKLLDAIRLRLRADVPVGVYISGGLDSSVIAALA 279 Query: 298 IR-HNPRLITFTTGFEREGFSEIDVAVASAEAIGARHIAKVVSADEFVAALPEIVWYLDE 356 + + +F F GF E A +G H + + AALP++V + + Sbjct: 280 RKLDTTSMHSFGVRFTDAGFDETPQQRLVAGHVGTGHHDILCGPRDIQAALPDVVRHSET 339 Query: 357 PVADPALVPLFFVAREARKH-VKVVLSGEGADELFGGYTIYREPLSLRPFDYLP------ 409 P+ A PLF ++R R+ ++VVLSGEGADE GY +++E R + P Sbjct: 340 PLVRTAPAPLFLLSRLVRESGIRVVLSGEGADEWLAGYDLFKEDKVRRFWARQPGSKVRP 399 Query: 410 ------KPLRRSMGKVSKPLPEGMRGKSLLHRGSLTLEERYYGNARSFSGAQLREVLPGF 463 P G+ PL ++ RG + +E +Y + + + L Sbjct: 400 KLLGRVHPFAAVNGQKDSPL-----WQAFFKRGMMETDEAFYAHRTRWRNTAWAQRLLSA 454 Query: 464 RPDWTHTDVTAPVYAES------AGWDPVARMQHIDLFTWLRGDIL-VKADKITMANSLE 516 T D + + + W P+AR Q ++ +++ +L + D++ MAN +E Sbjct: 455 DVQATADDAAFEAHVAAHLPDGWSRWSPLARSQWAEISSFMTPYLLSTQGDRVAMANGIE 514 Query: 517 LRVPFLDPEVFAVASRLPAGAKITRTTTKYALRRALEPIVPAHVLHRPKLGFPVPI 572 +R PFLDP V + + LP K+ K ALRR +PA ++ RPK + P+ Sbjct: 515 VRYPFLDPAVDDLCAALPDRVKMLGLRDKLALRRLAARHLPAEIVQRPKRPYRAPM 570 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: 1182 Number of extensions: 68 Number of successful extensions: 6 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: 684 Length adjustment: 38 Effective length of query: 614 Effective length of database: 646 Effective search space: 396644 Effective search space used: 396644 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 WP_012976121.1 AZL_RS19060 (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.7633.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-143 465.3 0.0 2e-143 465.0 0.0 1.0 1 lcl|NCBI__GCF_000010725.1:WP_012976121.1 AZL_RS19060 asparagine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000010725.1:WP_012976121.1 AZL_RS19060 asparagine synthase (glutamine-hydrolyzing) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 465.0 0.0 2e-143 2e-143 1 517 [] 2 566 .. 2 566 .. 0.93 Alignments for each domain: == domain 1 score: 465.0 bits; conditional E-value: 2e-143 TIGR01536 1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek 69 Cg+ag+++ +++ +++k+m+ +l+hRGPD+ g+++d ++ +l+h+RL+i+ l +g QP++ne+ lcl|NCBI__GCF_000010725.1:WP_012976121.1 2 CGVAGVLAGSRAEPAGLDELKRMIAMLSHRGPDGYGFYRD---DRIGLAHARLSIVGLAGGFQPIHNED 67 *********99877799***********************...8************************* PP TIGR01536 70 .evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelf 137 + +i fnGEI+Nh eLr++le++G++F t++DtEVi++a+ee+g ++ +rL+G+FA+ lwd+ ++el lcl|NCBI__GCF_000010725.1:WP_012976121.1 68 rSLWISFNGEIFNHVELRRDLEARGHRFYTRTDTEVIVHAFEEYGPATWARLNGQFAICLWDATRRELW 136 *9******************************************************************* PP TIGR01536 138 laRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepa 206 l+RDrlGi PL+ya+ +++l+faSE+Kal+ ++++++d++ la+++t+++ +++ ++f++v+ +++a lcl|NCBI__GCF_000010725.1:WP_012976121.1 137 LVRDRLGILPLFYARRGDHLVFASEAKALFGGGRVAPAFDHARLAQVFTHWSAAPHGSVFERVESVPAA 205 ***************************************************9999************** PP TIGR01536 207 kal..dgeeklee....ywevekee....vkeseeelveelrelledavkkrlvadvpvgvllSGGlDS 265 a d +l+ yw+ + ++ k s++e+ ++l+e+l da++ rl+advpvgv++SGGlDS lcl|NCBI__GCF_000010725.1:WP_012976121.1 206 TAIrvD--STLALhvdrYWQPDFTAdpalAKLSLDEAADRLEEKLLDAIRLRLRADVPVGVYISGGLDS 272 *99552..433333466****99999999999************************************* PP TIGR01536 266 slvaaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleep 334 s++aa+a+k +++++F ++f+ ++ +de+ ++r va ++gt h+ +l + ++ ++l++v+++ e p lcl|NCBI__GCF_000010725.1:WP_012976121.1 273 SVIAALARKLDTTSMHSFGVRFT-DAGFDETPQQRLVAGHVGTGHHDILCGPRDIQAALPDVVRHSETP 340 ***********************.********************************************* PP TIGR01536 335 tairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale................... 384 + +a +pl+lls+l+re g++VvLsGeGaDE ++GY+ f+e k+++ + lcl|NCBI__GCF_000010725.1:WP_012976121.1 341 LVRTAPAPLFLLSRLVRESGIRVVLSGEGADEWLAGYDLFKEDKVRRFWArqpgskvrpkllgrvhpfa 409 *************************************************99999999999988888877 PP TIGR01536 385 ...............lpeaselaekklllqaklakeselkellkakleeelkekeelkkelkee..... 433 ++e+ e+ +++++++++ ++ll+a+++++ +++ ++ lcl|NCBI__GCF_000010725.1:WP_012976121.1 410 avngqkdsplwqaffKRGMMETDEAFYAHRTRWRNTAWAQRLLSADVQATADDAAFEAHVAAHLpdgws 478 77777776666555322333355555599999****99*****99999887765544444444466799 PP TIGR01536 434 ..seleellrldlelllsdllrak..DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLr 498 s l++ + +++ +++ +l+ Drv+ma+++EvR+PflD ++ +l++ +p +k+ + K Lr lcl|NCBI__GCF_000010725.1:WP_012976121.1 479 rwSPLARSQWAEISSFMTPYLLSTqgDRVAMANGIEVRYPFLDPAVDDLCAALPDRVKMLGLRDKLALR 547 999**************99998888******************************************** PP TIGR01536 499 eaaeellPeeileRkKeaf 517 ++a+++lP ei++R+K+++ lcl|NCBI__GCF_000010725.1:WP_012976121.1 548 RLAARHLPAEIVQRPKRPY 566 ****************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (517 nodes) Target sequences: 1 (684 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: 00:00:00.03 # Mc/sec: 10.10 // [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