Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate GFF1957 HP15_1914 asparagine synthase, glutamine-hydrolyzing
Query= CharProtDB::CH_005185 (632 letters) >FitnessBrowser__Marino:GFF1957 Length = 632 Score = 353 bits (906), Expect = e-101 Identities = 218/638 (34%), Positives = 348/638 (54%), Gaps = 43/638 (6%) Query: 1 MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60 MCG G L ++M Q I HRGPD++G D+ V +RLSI+D+ + Sbjct: 1 MCGIAGFLRTGTLPDREQHHLWAERMGQAIAHRGPDANGVHIDQDVALVHQRLSILDLSS 60 Query: 61 GG-QPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAAS 119 G QP++ Y I+FNGEIYN+ LRE LE G++F T +DTEVLLA Y + E Sbjct: 61 AGNQPMASSCGRYIIVFNGEIYNFRSLREGLEQDGFSFKTQTDTEVLLALYARHGESCLR 120 Query: 120 KLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQ-NDIEIDK 178 +L GMFAF IW+ L+ RD G KPLYYT + Q +F SE K+L + Sbjct: 121 QLNGMFAFAIWDAKTKSLFIGRDRLGKKPLYYTDTDGQFFFGSEIKALFATPVVRPALRP 180 Query: 179 EALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANFKPVQTEEDKLV 238 +A++ + +Q++P+P T+ A+V K+ PG + +G I+ + Y+ +F+PV E + V Sbjct: 181 DAIKDFFVYQYIPDPKTIYANVHKLPPGHCMEV-CEGRISVRKYWDLSFRPV---EGRTV 236 Query: 239 KEVRDAIYD----SVNVHMRSDVPVGSFLSGGIDSSFIVS-VAKEFHPSLKTFSVGFEQQ 293 +++ +YD +V + M SDVP+G+FLSGGIDSS +V +A + T ++GF+ + Sbjct: 237 SDIKAGLYDVIDEAVRLRMISDVPLGAFLSGGIDSSAVVGLMAGRSSQPVTTCTIGFDDE 296 Query: 294 GFSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFVAKEAK 353 F E+ A A ++ + E + L I FD+P ADP+ +P +FV++ A+ Sbjct: 297 KFDEIKYADLVARQFKTDHHVFTVK-ETVADNLVGISRFFDEPFADPSFVPTFFVSQLAR 355 Query: 354 KHVTVALSGEGADELFGGYNIYREPL------SLKP---FERIPSGLKKMLLHVAAVMPE 404 VTVAL+G+G DE F GY+ YR SL P + GL ++ H+ P Sbjct: 356 TQVTVALAGDGGDENFAGYSKYRTDAIENRIRSLFPPALRHSLFPGLSRLAGHIPG--PL 413 Query: 405 GMRGKSLLERGCTPLQDRYIG--------NAKIFEESVKKQ---LLKHYNPNLSYRDVTK 453 G + SLL T D +G N ++++ V + L Y+P D+T+ Sbjct: 414 GKKASSLLG---TVALDPDLGFFTSNCFFNPRVWKRVVSPEFAALTDDYDP----ADITR 466 Query: 454 TYFTESSSYSDINKMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIP 513 ++ E+ + ++++ Y DI T++ GDIL+K D+M+MANSLE R P LD V + A+ IP Sbjct: 467 HHYQEAPAEDHLSRILYTDIKTYLPGDILVKVDRMSMANSLETRAPLLDYRVVEYAAGIP 526 Query: 514 DELKTKNGTTKYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNII--QESQ 571 LK K K++L++ ++ E +L RKK+GF VP+ WL++E+ ++ +S Sbjct: 527 SALKLKGNCKKHVLKECFSDLLDEDILYRKKMGFSVPLAQWLRSEIRAIAEPLLTGPDSG 586 Query: 572 TDAYIHKDYVLQLLEDHCADKADNSRKIWTVLIFMIWH 609 Y + V L + H + ++++W++++F +W+ Sbjct: 587 LSRYFRMEQVRALWQAHLSGDNRFTQELWSMVVFALWY 624 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: 984 Number of extensions: 43 Number of successful extensions: 7 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: 632 Length of database: 632 Length adjustment: 38 Effective length of query: 594 Effective length of database: 594 Effective search space: 352836 Effective search space used: 352836 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: 54 (25.4 bits)
Align candidate GFF1957 HP15_1914 (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.2488.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-153 496.5 0.0 7e-153 496.2 0.0 1.1 1 lcl|FitnessBrowser__Marino:GFF1957 HP15_1914 asparagine synthase, g Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF1957 HP15_1914 asparagine synthase, glutamine-hydrolyzing # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 496.2 0.0 7e-153 7e-153 1 517 [] 2 560 .. 2 560 .. 0.89 Alignments for each domain: == domain 1 score: 496.2 bits; conditional E-value: 7e-153 TIGR01536 1 Cgiagivdlkakake..eeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek.ev 71 Cgiag++ + ++ ++ +++m +++ahRGPDa+gv++d ++++l+h+RL+i dls++ +QP+++ ++ lcl|FitnessBrowser__Marino:GFF1957 2 CGIAGFLRTGTLPDReqHHLWAERMGQAIAHRGPDANGVHID---QDVALVHQRLSILDLSSAgNQPMASSCgRY 73 *******9988777654555689*******************...79*************9998*******99** PP TIGR01536 72 vivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGik 146 +ivfnGEIYN+++Lre le++G++F+t++DtEV+La+y +ge ++ +L+GmFAfa+wd+k++ lf+ RDrlG+k lcl|FitnessBrowser__Marino:GFF1957 74 IIVFNGEIYNFRSLREGLEQDGFSFKTQTDTEVLLALYARHGESCLRQLNGMFAFAIWDAKTKSLFIGRDRLGKK 148 *************************************************************************** PP TIGR01536 147 PLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal...dgeekleey 218 PLYy+ ++g+++f+SEiKal+a++ ++++l+ +a+++++ +q+ p++kt++++v++l+p++++ +g ++++y lcl|FitnessBrowser__Marino:GFF1957 149 PLYYTDTDGQFFFGSEIKALFATPVVRPALRPDAIKDFFVYQYIPDPKTIYANVHKLPPGHCMevcEGRISVRKY 223 ***************************************************************98888889999* PP TIGR01536 219 wevekee.vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsigfedskd 292 w+++ + ++++ ++ l + + +av+ r+++dvp+g++lSGG+DSs+v+ +++ + ++v+t +igf+ +++ lcl|FitnessBrowser__Marino:GFF1957 224 WDLSFRPvEGRTVSDIKAGLYDVIDEAVRLRMISDVPLGAFLSGGIDSSAVVGLMAGRSSQPVTTCTIGFD-DEK 297 ****999556678899999****************************************************.9** PP TIGR01536 293 ldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvLsGeGaDEl 367 +de k+a va+++ t+h+ +++ +e+v+++l + + ++ep+a+++ +p++++s+lar + v+V+L G+G+DE lcl|FitnessBrowser__Marino:GFF1957 298 FDEIKYADLVARQFKTDHHVFTV-KETVADNLVGISRFFDEPFADPSFVPTFFVSQLARTQ-VTVALAGDGGDEN 370 *******************9998.5799*********************************.************* PP TIGR01536 368 fgGYeyfreakaeeale.....................lpeaselaekkl......................... 396 f+GY+++r+ e++++ + lcl|FitnessBrowser__Marino:GFF1957 371 FAGYSKYRTDAIENRIRslfppalrhslfpglsrlaghI----------Pgplgkkassllgtvaldpdlgffts 435 *****************9998888888855544443331..........13333334455777778888888444 PP TIGR01536 397 ..llqaklakeselkellkakleeelke.keelkkelkeeseleellrldlelllsdllrak.DrvsmahslEvR 467 + + ++ k++++ e++ + +++ + ++++ +e ++e +l+++l+ d++++l++++++k Dr+sma+slE R lcl|FitnessBrowser__Marino:GFF1957 436 ncFFNPRVWKRVVSPEFAALTDDYDPADiTRHHYQEAPAEDHLSRILYTDIKTYLPGDILVKvDRMSMANSLETR 510 4433333333334444444333333333133444555666*********************************** PP TIGR01536 468 vPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517 +P+lD ++ve+a+ ip lkl+ +++K++L+e++ +ll e+il+RkK++f lcl|FitnessBrowser__Marino:GFF1957 511 APLLDYRVVEYAAGIPSALKLKGNCKKHVLKECFSDLLDEDILYRKKMGF 560 ************************************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (517 nodes) Target sequences: 1 (632 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: 7.89 // [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