Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_027178967.1 G496_RS0108840 asparagine synthase (glutamine-hydrolyzing)
Query= CharProtDB::CH_005185 (632 letters) >NCBI__GCF_000429985.1:WP_027178967.1 Length = 651 Score = 323 bits (829), Expect = 1e-92 Identities = 206/654 (31%), Positives = 343/654 (52%), Gaps = 54/654 (8%) Query: 1 MCGFVGVFNKHPLAQTADQEELIKQ---MNQMIVHRGPDSDGYFHDEHVGFGF--RRLSI 55 MCG G + L ++ D EEL ++ M + RGPD+D + D+ +G F RRL+I Sbjct: 1 MCGISGFID---LTRSLDSEELSRRAGLMGKSQQSRGPDADAQWVDQEIGIAFDHRRLAI 57 Query: 56 IDV-ENGGQPLSYEDETYWIIFNGEIYNYIELREELEAK-GYT-FNTDSDTEVLLATYRH 112 ID+ E G QP+ Y +FNGEIYNY ELR ELE G+ + SDTEVLL Sbjct: 58 IDLTEEGIQPMHSRSGRYVTVFNGEIYNYAELRSELETTAGFNGWRGHSDTEVLLEAIEQ 117 Query: 113 YK-EEAASKLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQ 171 + E++ + GMFA +W++ + L+ RD G KPL+Y D YFASE K++ + Sbjct: 118 WGLEKSLERFSGMFAIALWDRRERQLFLVRDRMGEKPLFYGRQGDTFYFASELKAIRQLE 177 Query: 172 N-DIEIDKEALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKANFKPV 230 + EI+++AL Y+ + +VP P T+ V + PG+ + DG ++ + + Sbjct: 178 SFKPEINRDALCSYLRYHYVPSPGTIYNKVSSLMPGTWIRVDYDGTVSGPFSYWSLKDCA 237 Query: 231 QTEED--------KLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFHPS 282 Q D ++ + D + + M SDVP+G+FLSGG+DSS IV++ ++ + Sbjct: 238 QKGVDLSFTASSGEITDTLEDLLLKVIEREMVSDVPLGAFLSGGVDSSLIVALMQQCALA 297 Query: 283 -LKTFSVGFEQQGFSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPA 341 +KTF++GF+ + ++E + A + AA +G E+ ++P + ++ +PKI +D P +D + Sbjct: 298 PVKTFTIGFDDKAYNEAEEAAKVAAYIGTEHTELYVTPADALDVIPKIPKIWDQPFSDAS 357 Query: 342 AIPLYFVAKEAKKHVTVALSGEGADELFGGYNIYREPLSL-KPFERIPSGLKKMLLH--- 397 +P + V+ +KHVTVALSG+G DELF GYN + + L +P G++K Sbjct: 358 QVPTHLVSMMTRKHVTVALSGDGGDELFAGYNRHFKGCGLWDKLASVPPGIRKFTAESLQ 417 Query: 398 -------------VAAVMPEGMR----GKSLLERG----CTPLQDRYIGNAKIFEESVKK 436 + V+P ++ G+ L + +D Y+ + + K Sbjct: 418 KVPANEWNAFFEIIDPVLPRKLKMRLPGQKLHKLADVMTAASARDYYLKLTSNWFDPEKL 477 Query: 437 QLLKHYNPNLSYRDVTKTYFTESSSYSDINKMQYVDIHTWMRGDILLKADKMTMANSLEL 496 + +P V + E+S ++ MQ++D T++ DI+ K D+ MA SLE Sbjct: 478 VINGWEHPGPYQSPVNQ---PETSCLTE--WMQFMDAATYLPDDIMTKVDRAAMAVSLET 532 Query: 497 RVPFLDKVVFDVASKIPDELKTKNGTTKYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLK 556 R PFLD + + + ++P LK ++G K +LR VP+ ++ R K+GF +PI WL+ Sbjct: 533 RAPFLDHEIVEFSQRLPMSLKIQHGRGKKILRDILYKYVPQRLIERPKMGFGIPIDSWLR 592 Query: 557 NEMNEWVRNIIQ--ESQTDAYIHKDYVLQLLEDHCADKADNSRKIWTVLIFMIW 608 + +WV +++ + Y+H + + ++ DH + K D KIW +L+F W Sbjct: 593 GPLRDWVEDLLNPVRMMNEGYLHPEPIRKMWADHLSGKTDAQYKIWNILVFQSW 646 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: 1038 Number of extensions: 57 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: 651 Length adjustment: 38 Effective length of query: 594 Effective length of database: 613 Effective search space: 364122 Effective search space used: 364122 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_027178967.1 G496_RS0108840 (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.3821051.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-142 460.4 0.0 7.9e-142 459.7 0.0 1.3 1 NCBI__GCF_000429985.1:WP_027178967.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000429985.1:WP_027178967.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 459.7 0.0 7.9e-142 7.9e-142 1 517 [] 2 583 .. 2 583 .. 0.85 Alignments for each domain: == domain 1 score: 459.7 bits; conditional E-value: 7.9e-142 TIGR01536 1 Cgiagivdlkakake..eeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek. 69 Cgi g++dl++ +++ ++ + m + ++ RGPDa++ w d +e + ++ hrRLaiidl e QP+++++ NCBI__GCF_000429985.1:WP_027178967.1 2 CGISGFIDLTRSLDSeeLSRRAGLMGKSQQSRGPDADAQWVD-QEIGIAFDHRRLAIIDLTEEgIQPMHSRSg 73 ***********9999754567778889999************.799**************8877********* PP TIGR01536 70 evvivfnGEIYNheeLreelee.kGye.FetksDtEViLaayeewg.eelverLeGmFAfalwdekkgelfla 139 ++v vfnGEIYN+ eLr ele+ +G++ ++++sDtEV+L+a+e+wg e+ +er+ GmFA+alwd+++++lfl+ NCBI__GCF_000429985.1:WP_027178967.1 74 RYVTVFNGEIYNYAELRSELETtAGFNgWRGHSDTEVLLEAIEQWGlEKSLERFSGMFAIALWDRRERQLFLV 146 ********************96268765899****************************************** PP TIGR01536 140 RDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal..d 210 RDr+G kPL+y++++++++faSE+Ka+ +l+++k+e++++al ++l +++vp++ t++++v l+p+ d NCBI__GCF_000429985.1:WP_027178967.1 147 RDRMGEKPLFYGRQGDTFYFASELKAIRQLESFKPEINRDALCSYLRYHYVPSPGTIYNKVSSLMPGTWIrvD 219 ********************************************************************99775 PP TIGR01536 211 geeklee...ywevekee.......vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiak 273 + +++ yw++++ + +++s e +++l++ll + +++ +v+dvp+g++lSGG+DSsl++a+++ NCBI__GCF_000429985.1:WP_027178967.1 220 YDGTVSGpfsYWSLKDCAqkgvdlsFTASSGEITDTLEDLLLKVIEREMVSDVPLGAFLSGGVDSSLIVALMQ 292 5555555788****9988899999999999******************************************* PP TIGR01536 274 keaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyll 346 + a ++vktF+igf+ +k+++e++ a+kva+++gteh+e++++++++l+ ++++ ++++p+++++++p+ l+ NCBI__GCF_000429985.1:WP_027178967.1 293 QCALAPVKTFTIGFD-DKAYNEAEEAAKVAAYIGTEHTELYVTPADALDVIPKIPKIWDQPFSDASQVPTHLV 364 ***************.9******************************************************** PP TIGR01536 347 sklarekgvkVvLsGeGaDElfgGYeyfrea..kaeeale......................lpeaselaekk 395 s ++r++ v+V+LsG+G+DElf+GY+++++ +++ + NCBI__GCF_000429985.1:WP_027178967.1 365 SMMTRKH-VTVALSGDGGDELFAGYNRHFKGcgLWDKLASvppgirkftaeslqkvpanewnA---------- 426 *******.*******************998522455555566666666555555554444440.......... PP TIGR01536 396 l..................................llqaklakeselkellkakleeelkekeelkkelkee. 433 + ++ kl++++ NCBI__GCF_000429985.1:WP_027178967.1 427 FfeiidpvlprklkmrlpgqklhkladvmtaasarDYYLKLTSNW--------------------------Fd 473 055555533333333333333343333222222221222222222..........................02 PP TIGR01536 434 .........................seleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelal 480 +e ++ d++++l+d++ k Dr++ma slE R+PflD+e+ve+ NCBI__GCF_000429985.1:WP_027178967.1 474 peklvingwehpgpyqspvnqpetsCLTEWMQFMDAATYLPDDIMTKvDRAAMAVSLETRAPFLDHEIVEFSQ 546 222223333333444455556665477788999**************************************** PP TIGR01536 481 sippelklrdgkeKvlLreaaeellPeeileRkKeaf 517 ++p++lk+++g+ K +Lr ++ +++P+++ eR+K++f NCBI__GCF_000429985.1:WP_027178967.1 547 RLPMSLKIQHGRGKKILRDILYKYVPQRLIERPKMGF 583 ***********************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (517 nodes) Target sequences: 1 (651 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: 00:00:00.02 # Mc/sec: 12.17 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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