Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_092994041.1 BLP65_RS06145 asparagine synthase (glutamine-hydrolyzing)
Query= CharProtDB::CH_005185 (632 letters) >NCBI__GCF_900102855.1:WP_092994041.1 Length = 659 Score = 290 bits (741), Expect = 2e-82 Identities = 190/605 (31%), Positives = 311/605 (51%), Gaps = 34/605 (5%) Query: 1 MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60 MCG G+ N A EL M + HRGPD VG RLSIID+E Sbjct: 1 MCGIAGILNLRRGAPAVGSLEL-GAMIAPLAHRGPDGADVRRFGPVGLAHARLSIIDLEG 59 Query: 61 GGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAASK 120 G QPL+ ED + W++ NGEI+N+ ELR++L++ G++F T+SDTEV++ Y + E + Sbjct: 60 GKQPLANEDGSIWVVLNGEIFNFPELRQQLKSAGHSFRTESDTEVIVHLYEDHGEAFVHQ 119 Query: 121 LRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQNDI-EIDKE 179 L G FA +W+ L RD GI PL+Y+ ++++FASE K++ Q + E Sbjct: 120 LNGQFAIALWDSVQEKLVLVRDRVGIAPLFYSEEGERLFFASEVKAIQPVQKRTPRANLE 179 Query: 180 ALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANFKPVQT----EED 235 AL+Q M++ P+TL V ++ PG T+ +G ++ Y+ ++ T E+ Sbjct: 180 ALEQVMTYWAPLSPNTLFEGVHELPPGHLMTVE-NGKMSLHRYWDWSYPSDGTYDERNEE 238 Query: 236 KLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFHPS-LKTFSVGFEQQG 294 +L +E+R + D+V + +RSDVPVG++LSGG+DSS I ++ ++ + LKTFS+GF+Q+G Sbjct: 239 ELAEELRSLLADAVRIRLRSDVPVGAYLSGGLDSSAIAALIRQADSAPLKTFSIGFDQEG 298 Query: 295 FSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFVAKEAKK 354 + E D E + LG + S + P+ +WH + PL A P+ ++ + Sbjct: 299 YDESDYQAEMVSHLGTRHRSFQCGLSDISESFPETIWHAETPLLRTAPTPMKLLSGHVRD 358 Query: 355 H-VTVALSGEGADELFGGYNIYREPLSLKPFERIPSG------LKKMLLHVAAVMPEGMR 407 V L+GEGADE+ GGY+I++E + + R P LK++ ++ + + Sbjct: 359 EGYKVVLTGEGADEVLGGYDIFKEAKIRQFWSRNPDSKFRPALLKRLYPYLNIAGGQSLA 418 Query: 408 G-KSLLERGCTPLQDRYIGNAK----------IFEESVKKQLLKHYNPNLSYRDVTKTYF 456 K RG + + F E +++ +L Y S R + F Sbjct: 419 YLKQFFGRGLHEPDSPWFSHVPRWTTTGATKGFFSERMQEYVLSGYE---SARSLLPAEF 475 Query: 457 TESSSYSDINKMQYVDIHTWMRGDILL-KADKMTMANSLELRVPFLDKVVFDVASKIPDE 515 + K QY++ T M G +L + D+M MAN +E R PFLD + + A++I Sbjct: 476 DR---WHWFEKAQYIESKTLMAGYLLCSQGDRMLMANGVEGRYPFLDHRIIEFANRIHPR 532 Query: 516 LKTKNGTTKYLLRKAAEGIVPEHVLNRKKLGFPVP-IRHWLKNEMNEWVRNIIQESQTDA 574 LK + T KYLL+KA +P+ + R K + P +L ++ E++ +++ + Sbjct: 533 LKMRGLTEKYLLKKAVGRYLPKRIAERTKQPYRAPESAPFLNRQVPEFIHEMMKPEKLRD 592 Query: 575 YIHKD 579 Y + D Sbjct: 593 YGYFD 597 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: 1016 Number of extensions: 50 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 632 Length of database: 659 Length adjustment: 38 Effective length of query: 594 Effective length of database: 621 Effective search space: 368874 Effective search space used: 368874 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 WP_092994041.1 BLP65_RS06145 (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.10089.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-153 498.7 0.0 1.4e-153 498.5 0.0 1.0 1 lcl|NCBI__GCF_900102855.1:WP_092994041.1 BLP65_RS06145 asparagine synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900102855.1:WP_092994041.1 BLP65_RS06145 asparagine synthase (glutamine-hydrolyzing) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 498.5 0.0 1.4e-153 1.4e-153 1 517 [] 2 564 .. 2 564 .. 0.90 Alignments for each domain: == domain 1 score: 498.5 bits; conditional E-value: 1.4e-153 TIGR01536 1 Cgiagivdlkakake.eeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsne 68 Cgiagi++l++ a + ++ +m+ lahRGPD+ v + ++l+h+RL+iidl++g+QPl+ne lcl|NCBI__GCF_900102855.1:WP_092994041.1 2 CGIAGILNLRRGAPAvGSLELGAMIAPLAHRGPDGADV--R-RFGPVGLAHARLSIIDLEGGKQPLANE 67 *********99998888899****************95..3.569************************ PP TIGR01536 69 k.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgel 136 + + ++v nGEI+N+ eLr++l+ +G++F+t+sDtEVi+++ye +ge++v++L+G+FA+alwd+ +++l lcl|NCBI__GCF_900102855.1:WP_092994041.1 68 DgSIWVVLNGEIFNFPELRQQLKSAGHSFRTESDTEVIVHLYEDHGEAFVHQLNGQFAIALWDSVQEKL 136 ********************************************************************* PP TIGR01536 137 flaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelep 205 +l+RDr+Gi PL+y++e+++l+faSE+Ka+ ++++ +++ + eal +++t++ +++tlf++v+el+p lcl|NCBI__GCF_900102855.1:WP_092994041.1 137 VLVRDRVGIAPLFYSEEGERLFFASEVKAIQPVQKRTPRANLEALEQVMTYWAPLSPNTLFEGVHELPP 205 ****************************************************9999************* PP TIGR01536 206 akal...dgeekleeywevekee....vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSsl 267 ++ + +g+ +l++yw+ ++++ + +eeel eelr+ll dav+ rl++dvpvg++lSGGlDSs+ lcl|NCBI__GCF_900102855.1:WP_092994041.1 206 GHLMtveNGKMSLHRYWDWSYPSdgtyDERNEEELAEELRSLLADAVRIRLRSDVPVGAYLSGGLDSSA 274 ***998888889999******999998888999************************************ PP TIGR01536 268 vaaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleepta 336 +aa++++ +++ktFsigf+ ++ +des+++++++ +lgt+h++++ ++ + ++e i++ e p+ lcl|NCBI__GCF_900102855.1:WP_092994041.1 275 IAALIRQADSAPLKTFSIGFD-QEGYDESDYQAEMVSHLGTRHRSFQCGLSDISESFPETIWHAETPLL 342 ********99***********.*********************************************** PP TIGR01536 337 irasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale..................... 384 +a +p+ lls +r++g+kVvL+GeGaDE++gGY++f+eak ++ + lcl|NCBI__GCF_900102855.1:WP_092994041.1 343 RTAPTPMKLLSGHVRDEGYKVVLTGEGADEVLGGYDIFKEAKIRQFWSrnpdskfrpallkrlypylni 411 ***********************************************9999999988888888777665 PP TIGR01536 385 .........lpeaselaekkl..............llqaklakeselkellkakleeelke.....kee 425 + + +++++ ++k +++++++e + + ++ lcl|NCBI__GCF_900102855.1:WP_092994041.1 412 aggqslaylK----------QffgrglhepdspwfSHVPRWTTTGATKGFFSERMQEYVLSgyesaRSL 470 5555533330..........1345555566666664445555555555555555554443300000333 PP TIGR01536 426 lkkelkeeseleellrldlelllsdllrak..DrvsmahslEvRvPflDkelvelalsippelklrdgk 492 l +e+ + + +e++++ + ++l+ ++l+ + Dr++ma+++E R+PflD++++e+a +i p lk+r + lcl|NCBI__GCF_900102855.1:WP_092994041.1 471 LPAEFDRWHWFEKAQYIESKTLMAGYLLCSqgDRMLMANGVEGRYPFLDHRIIEFANRIHPRLKMRGLT 539 4444444499******************999************************************** PP TIGR01536 493 eKvlLreaaeellPeeileRkKeaf 517 eK+lL++a+ ++lP++i+eR K+++ lcl|NCBI__GCF_900102855.1:WP_092994041.1 540 EKYLLKKAVGRYLPKRIAERTKQPY 564 **********************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (517 nodes) Target sequences: 1 (659 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 9.16 // [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