Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_043745402.1 AMB_RS20340 asparagine synthase (glutamine-hydrolyzing)
Query= CharProtDB::CH_005185 (632 letters) >NCBI__GCF_000009985.1:WP_043745402.1 Length = 635 Score = 313 bits (801), Expect = 2e-89 Identities = 213/640 (33%), Positives = 329/640 (51%), Gaps = 40/640 (6%) Query: 1 MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVG--FGFRRLSIIDV 58 MCGF G + T D+E +++ M +VHRGPD DG + D+ G GFRRL+IID+ Sbjct: 1 MCGFAGFLDL--TRATPDRETVVRAMAATLVHRGPDDDGAWVDDDAGVALGFRRLAIIDL 58 Query: 59 E-NGGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEA 117 G QP++ D + I FNGEIYN+ +LR L + + SDTEVLL + EA Sbjct: 59 TPQGHQPMTSHDGRWVISFNGEIYNHADLRARL-GESMAWRGHSDTEVLLEAVSAWGIEA 117 Query: 118 A-SKLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQNDIE- 175 A + GMFAF +W++ + VL ARD FG KPLY+ + F SE K+L Sbjct: 118 ALAAFDGMFAFALWDRRERVLTLARDRFGEKPLYWAKAGGSLLFGSELKALRAHPAWTGG 177 Query: 176 IDKEALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANFKPVQTEE- 234 ID++AL YM ++P P T+ V K+EPG + GDI+ K Y+ A E+ Sbjct: 178 IDRDALALYMRLGWIPAPHTIHPGVFKLEPGHLMRVN-GGDISAKAYWSAADCAAGLEDS 236 Query: 235 -----DKLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFHPS-LKTFSV 288 + + + + +SV + M++DVPVG FLSGGIDSS ++ ++ + +F++ Sbjct: 237 FAGSAEDAADRLEELLRESVRLRMQADVPVGVFLSGGIDSSATAALMRQLSAEPVHSFTI 296 Query: 289 GFEQQGFSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFV 348 GF+Q G E A+ A LG + IS E + ++ ++ +D+P AD AA+P + Sbjct: 297 GFDQAGLDESAHARAVADHLGTLHTEVRISDAEALAQVARLPVLYDEPFADAAALPTALL 356 Query: 349 AKEAKKHVTVALSGEGADELFGGYNIYRE-PLSLKPFERIPSGLKKMLLHVAAVMPEGMR 407 A+ +K VTVALSG+GADELFGGY IYR P + + +P GL+ + A+ G+ Sbjct: 357 AQVTRKSVTVALSGDGADELFGGYGIYRSIPRDWRRLQGLPDGLRAL----GAMGARGLA 412 Query: 408 G--KSLLERGCTPLQDRYIGNAKIFEE-------SVKKQLLKHYNPNLSYRDVTKTYFTE 458 G + L T + R ++ E S+ + L HY+ D+ Sbjct: 413 GPAEGLAALAGTVRKRRSHPGHRLGREAERLEAGSLAELLGLHYSRWRGMSDLVPGAGRA 472 Query: 459 SSSYS--------DINKMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVAS 510 S +S D +D ++ D+ +K D+ TM SLE R+PFL + A Sbjct: 473 ESLFSAPTPRLHDDALATMVLDAMGYLPDDLCVKTDRATMGASLEARLPFLALDIARFAW 532 Query: 511 KIPDELKTKNGTTKYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQES 570 +P LK + T K +LR+ +VP +++R K+GF VP+R WL + +W +++ E Sbjct: 533 SLPTSLKIEGETGKAVLRRVLYRLVPRALVDRPKMGFEVPLRRWLNGPLRDWADDLLSEE 592 Query: 571 --QTDAYIHKDYVLQLLEDHCADKADNSRKIWTVLIFMIW 608 + +++ V Q +H + + ++W L+F W Sbjct: 593 RLRRQGHLNAALVAQCWREHRSGAKNWQNEMWHALMFQAW 632 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: 851 Number of extensions: 40 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 632 Length of database: 635 Length adjustment: 38 Effective length of query: 594 Effective length of database: 597 Effective search space: 354618 Effective search space used: 354618 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_043745402.1 AMB_RS20340 (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.1350.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-146 473.6 0.0 6e-146 473.3 0.0 1.1 1 lcl|NCBI__GCF_000009985.1:WP_043745402.1 AMB_RS20340 asparagine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_043745402.1 AMB_RS20340 asparagine synthase (glutamine-hydrolyzing) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 473.3 0.0 6e-146 6e-146 1 517 [] 2 569 .. 2 569 .. 0.90 Alignments for each domain: == domain 1 score: 473.3 bits; conditional E-value: 6e-146 TIGR01536 1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsne 68 Cg+ag++dl++++ ++e +++m+ tl hRGPD++g w d ++++++lg+rRLaiidl + +QP+ ++ lcl|NCBI__GCF_000009985.1:WP_043745402.1 2 CGFAGFLDLTRATPDRETVVRAMAATLVHRGPDDDGAWVD-DDAGVALGFRRLAIIDLTPQgHQPMTSH 69 ***********999999***********************.89***************9888******* PP TIGR01536 69 k.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewg.eelverLeGmFAfalwdekkge 135 + + vi fnGEIYNh +Lr++l e + ++++sDtEV+L+a +wg e++++ ++GmFAfalwd++++ lcl|NCBI__GCF_000009985.1:WP_043745402.1 70 DgRWVISFNGEIYNHADLRARLGES-MAWRGHSDTEVLLEAVSAWGiEAALAAFDGMFAFALWDRRERV 137 *99999*****************99.******************************************* PP TIGR01536 136 lflaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkele 204 l laRDr+G kPLY a+ +g+llf+SE+Kal a+++ + +d++ala ++ l + p ++t++ +v++le lcl|NCBI__GCF_000009985.1:WP_043745402.1 138 LTLARDRFGEKPLYWAKAGGSLLFGSELKALRAHPAWTGGIDRDALALYMRLGWIPAPHTIHPGVFKLE 206 ********************************************************************* PP TIGR01536 205 pakal...dgeekleeywevekee......vkeseeelveelrelledavkkrlvadvpvgvllSGGlD 264 p++ + g+ + + yw++++ + ++ s e++ ++l+ell+++v+ r+ advpvgv+lSGG+D lcl|NCBI__GCF_000009985.1:WP_043745402.1 207 PGHLMrvnGGDISAKAYWSAADCAagledsFAGSAEDAADRLEELLRESVRLRMQADVPVGVFLSGGID 275 ****987445555666****999889999999************************************* PP TIGR01536 265 SslvaaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilalee 333 Ss+ aa++++ ++++v++F+igf+ ++ ldes++ar+vad+lgt h+ev is +e+l++++++ + +e lcl|NCBI__GCF_000009985.1:WP_043745402.1 276 SSATAALMRQLSAEPVHSFTIGFD-QAGLDESAHARAVADHLGTLHTEVRISDAEALAQVARLPVLYDE 343 ************************.******************************************** PP TIGR01536 334 ptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale.................. 384 p+a++a+ p+ ll++ +r+ v+V+LsG+GaDElfgGY ++r +++ ++ lcl|NCBI__GCF_000009985.1:WP_043745402.1 344 PFADAAALPTALLAQVTRKS-VTVALSGDGADELFGGYGIYRSIPRD--WRrlqglpdglralgamgar 409 ********************.**********************8655..44445999999999888888 PP TIGR01536 385 ...............lpeaselaekkl.......llqaklakeselkellkakleeelkekeelkkelk 431 + + k+ +a+ ++ +l+ell ++++ + ++ + ++ lcl|NCBI__GCF_000009985.1:WP_043745402.1 410 glagpaeglaalagtV----R---KRRshpghrlGREAERLEAGSLAELLGLHYSRWRGMSDLVPGAGR 471 8888877755533221....1...111345555533344444555555666666655555555555544 PP TIGR01536 432 ee...........seleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelkl 488 +e + +++ ld+ +l+d+l +k Dr++m slE+R Pfl +++++a+s+p++lk+ lcl|NCBI__GCF_000009985.1:WP_043745402.1 472 AEslfsaptprlhDDALATMVLDAMGYLPDDLCVKtDRATMGASLEARLPFLALDIARFAWSLPTSLKI 540 4445666888888777788999999******************************************** PP TIGR01536 489 rdgkeKvlLreaaeellPeeileRkKeaf 517 + ++ K +Lr+++ +l+P+++++R+K++f lcl|NCBI__GCF_000009985.1:WP_043745402.1 541 EGETGKAVLRRVLYRLVPRALVDRPKMGF 569 ***************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (517 nodes) Target sequences: 1 (635 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: 00:00:00.02 # Mc/sec: 12.87 // [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