Align asparagine synthase (glutamine-hydrolysing) 3; EC 6.3.5.4 (characterized)
to candidate WP_029908049.1 P166_RS0101425 N-acetylglutaminylglutamine amidotransferase
Query= CharProtDB::CH_007942 (614 letters) >NCBI__GCF_000711315.1:WP_029908049.1 Length = 601 Score = 261 bits (666), Expect = 8e-74 Identities = 192/630 (30%), Positives = 306/630 (48%), Gaps = 62/630 (9%) Query: 1 MCGITGWVDFKKQLVQEKQTMDRMTDTLSKRGPDDSNVWGEHHVLFGHKRLAVVDI-EGG 59 MCGI G + + + V E ++ M L +RGPDD W ++ V GH+RL+++D+ + G Sbjct: 1 MCGICGEIYWNGRGVSEA-SLTPMLKALERRGPDDGGTWIQNQVGLGHRRLSIIDLSDAG 59 Query: 60 RQPMACTYKGDTYTIIYNGELYNTEDLRKELRARGHQFERTSDTEVLLHSYIEWQEDCVD 119 QPM + ++++NG +YN + LR L GH+F SDTEV+L +Y +W DCV Sbjct: 60 HQPMI----DNELSLVFNGCIYNYQSLRSLLIELGHEFCSHSDTEVILKAYRQWGMDCVT 115 Query: 120 HLNGIFAFAVWDEKRNLLFAARDRLGVKPFFYTKEGSSFLFGSEIKAILAHPDIKARVDR 179 G+FAFAVWD+ L ARDR G+KP +Y F S +A+LA DI +D Sbjct: 116 RFEGMFAFAVWDDHHQQLLIARDRFGIKPLYYAPVDGGVKFASNTQALLASGDINTEIDP 175 Query: 180 TGLSEIFGL-GPSRTPGTGIFKGIKEIRPAHALTFSKDGLNIWR-YWNVESEKHTD---- 233 GL F L G P T I KGI+++ P H + + DG + YW++ +E+ Sbjct: 176 IGLHHQFTLHGVIPAPYT-ILKGIRKLEPGHWMIVNPDGQMFKKSYWHLMAERPAGAENL 234 Query: 234 SFDDTVANVRSLFQDAVTRQL-VSDVPVCTFLSGGLDSSAITAIAAGHFEKEGKAPLHTY 292 + +D + + + AV ++L +DVPV LSGGLDSS I A+ A + G + T+ Sbjct: 235 NEEDWINRIHDSLKQAVHKRLTAADVPVGVLLSGGLDSSLIVALLA----EAGVENIRTF 290 Query: 293 SIDYEENDKYFQASAFQPNDDGPWIEKMTEAFGTTHHKCVISQKDLVDHLEEAVLVKDLP 352 SI +E+ + + S F+ +D ++ E + T H K +IS ++++ L AV P Sbjct: 291 SIGFEDVPEE-KGSEFEYSD------QVVERYQTIHKKYLISNEEVLPRLPGAVDAMAEP 343 Query: 353 GMADVDSSLLWFCREIKKDFVVSLSGECADEIFGGYPWF--------------HTADVES 398 + ++ KD V +SG+ ADE+F GY W+ + + Sbjct: 344 MFGQDAVAFYLLSEQVSKDVKVVMSGQGADEVFAGYFWYPQMAEAYEKLSPGEPPVNAFA 403 Query: 399 GFPWMRSTEERIKLLSDSWQKKLNLKEYVNAKYEETLAETPLLDGETGVDKARRQLFYLN 458 F + R+ EE +++++ + E+ N + E A T LD +D + Sbjct: 404 PFYFDRTHEEWLEMVNPKYHVHDVTSEWANDRLSEPGA-TTFLDQVLRLDAS-------- 454 Query: 459 MLWFMTNLLDRKDRMSMGASLEVRVPFADHRLVEYVWNIPWEMKMHDNREKGILRKALEG 518 + + + R D M+M SLE RVPF DH LVE + P +K D K +L+K G Sbjct: 455 -TLIVDDPVKRVDNMTMAWSLEARVPFLDHDLVELTMSAPESLKRKD--FKYVLKKIARG 511 Query: 519 ILPDDILYRKKSPYPKTHHPEYTKGVSEWLKTIRSQKDSVLHTLLDRKQLDQLL---ETE 575 I+PD ++ R K +P +W+K + + + + + ++ LL E E Sbjct: 512 IVPDSVIDRPKGYFPMPALKYVRDDFYQWMKDVLTSDAAKTRGIFNPDYIENLLANPENE 571 Query: 576 GSSFKVPWFGQLMKGPQLIAHLAQIHTWFE 605 S + KG +L H A + W + Sbjct: 572 ASFTAI-------KGSKL-WHAALLELWLQ 593 Lambda K H 0.320 0.137 0.425 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: 969 Number of extensions: 50 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: 614 Length of database: 601 Length adjustment: 37 Effective length of query: 577 Effective length of database: 564 Effective search space: 325428 Effective search space used: 325428 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 (21.8 bits) S2: 53 (25.0 bits)
Align candidate WP_029908049.1 P166_RS0101425 (N-acetylglutaminylglutamine amidotransferase)
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.19872.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-138 449.0 0.0 1.7e-138 448.7 0.0 1.0 1 lcl|NCBI__GCF_000711315.1:WP_029908049.1 P166_RS0101425 N-acetylglutaminy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000711315.1:WP_029908049.1 P166_RS0101425 N-acetylglutaminylglutamine amidotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 448.7 0.0 1.7e-138 1.7e-138 1 516 [. 2 524 .. 2 525 .. 0.86 Alignments for each domain: == domain 1 score: 448.7 bits; conditional E-value: 1.7e-138 TIGR01536 1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsne 68 Cgi g + + ++ e+ + ml++l++RGPD+ g+w++ ++++lghrRL+iidls++ +QP+ ++ lcl|NCBI__GCF_000711315.1:WP_029908049.1 2 CGICGEIYWNGRGVS-EASLTPMLKALERRGPDDGGTWIQ---NQVGLGHRRLSIIDLSDAgHQPMIDN 66 999998877776555.589*********************...79**************999******9 PP TIGR01536 69 kevvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelf 137 + +vfnG IYN+++Lr l+e G+eF ++sDtEViL+ay++wg ++v r+eGmFAfa+wd+++++l+ lcl|NCBI__GCF_000711315.1:WP_029908049.1 67 E-LSLVFNGCIYNYQSLRSLLIELGHEFCSHSDTEVILKAYRQWGMDCVTRFEGMFAFAVWDDHHQQLL 134 9.78***************************************************************** PP TIGR01536 138 laRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlq.lvptektlfkevkelep 205 +aRDr+GikPLYya +g + faS +alla +i++e+d +l++++tl+ + p + t+ k++++lep lcl|NCBI__GCF_000711315.1:WP_029908049.1 135 IARDRFGIKPLYYAPVDGGVKFASNTQALLASGDINTEIDPIGLHHQFTLHgVIPAPYTILKGIRKLEP 203 **************************************************9999*************** PP TIGR01536 206 akal....dgeekleeywevekee....vkeseeelveelrelledavkkrlv.advpvgvllSGGlDS 265 ++ + dg+ +++yw++ e+ + +ee+ ++++ + l++av+krl advpvgvllSGGlDS lcl|NCBI__GCF_000711315.1:WP_029908049.1 204 GHWMivnpDGQMFKKSYWHLMAERpagaENLNEEDWINRIHDSLKQAVHKRLTaADVPVGVLLSGGLDS 272 ***9996555555566***999888887788899******************989************** PP TIGR01536 266 slvaaiakkeaksevktFsigfe..dskdldeskaarkvadelgtehkevliseeevlkeleevilale 332 sl++a++++ ++++tFsigfe +++ +e ++ +v++ t hk++lis+eevl l+ + a+ lcl|NCBI__GCF_000711315.1:WP_029908049.1 273 SLIVALLAEAGVENIRTFSIGFEdvPEEKGSEFEYSDQVVERYQTIHKKYLISNEEVLPRLPGAVDAMA 341 ******9999999**********333444455669********************************** PP TIGR01536 333 eptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeealelpease.laekkl.... 396 ep+ ++++ ylls++++++ vkVv+sG+GaDE+f+GY ++ ++ + + +l+ + +++ + lcl|NCBI__GCF_000711315.1:WP_029908049.1 342 EPMFGQDAVAFYLLSEQVSKD-VKVVMSGQGADEVFAGYFWYPQMAEA-YEKLSPGEPpVNA--Fapfy 406 ********************9.********************996333.3332222222222..22333 PP TIGR01536 397 ..llqaklakeselkellkakleeelke.keelkkelkeeseleellrldlelllsdl.lrakDrvsma 461 ++++++ + ++ k ++ + ++e ++ +e +++ l+++lrld+ +l+ d+ +++ D ++ma lcl|NCBI__GCF_000711315.1:WP_029908049.1 407 fdRTHEEWLEMVNPKYHVH----DVTSEwANDRLSEPGATTFLDQVLRLDASTLIVDDpVKRVDNMTMA 471 3333333433333333333....22222022233333344889*******9988776626666****** PP TIGR01536 462 hslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKea 516 +slE+RvPflD++lvel +s p +lk ++ K++L+++a++++P+++ +R+K lcl|NCBI__GCF_000711315.1:WP_029908049.1 472 WSLEARVPFLDHDLVELTMSAPESLKR--KDFKYVLKKIARGIVPDSVIDRPKGY 524 ***********************9875..678********************965 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (517 nodes) Target sequences: 1 (601 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: 8.68 // [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