Align asparagine synthetase B, glutamine-hydrolyzing; EC 6.3.5.4 (characterized)
to candidate 350079 BT0551 asparagine synthetase B [glutamine-hydrolyzing] (NCBI ptt file)
Query= CharProtDB::CH_002444 (554 letters) >FitnessBrowser__Btheta:350079 Length = 559 Score = 758 bits (1957), Expect = 0.0 Identities = 362/554 (65%), Positives = 445/554 (80%), Gaps = 1/554 (0%) Query: 1 MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGA 60 MC I G+ +IKT ELR KAL++++ +RHRGPDWSGIY +AILAHERLSIVD +G Sbjct: 1 MCGIAGILNIKTQTKELRDKALKMAQKIRHRGPDWSGIYVGGSAILAHERLSIVDPQSGG 60 Query: 61 QPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPEFLDDLQG 120 QPLY+ + LAVNGEIYNH+ +RA Y +Y FQTGSDCEVILALY++KG FL+++ G Sbjct: 61 QPLYSPDRKQALAVNGEIYNHRDIRARYAGQYDFQTGSDCEVILALYKDKGIHFLEEISG 120 Query: 121 MFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIKEFPAGSY 180 +FAF LYD EKD +LI RD +G+IPLY+G D+ G++Y SE+KAL C + F G Y Sbjct: 121 IFAFVLYDEEKDEFLIARDPIGVIPLYIGKDKDGKIYFGSELKALEGFCNEYEPFLPGHY 180 Query: 181 LWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVLLSGGLDS 240 +S++G+++ +Y R+W DY++VKDN +++++ALED+V LMSDVPYGVLLSGGLDS Sbjct: 181 FYSKEGKMKRWYTREWTDYESVKDNDAKVSDVKEALEDAVHRQLMSDVPYGVLLSGGLDS 240 Query: 241 SIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTVHHEIHF 300 S+ISAI KKYAA+R+E S+AWWPQLHSFA+GL G+PDL A+EVA ++GTVHHEI++ Sbjct: 241 SVISAIAKKYAAKRIETDGASDAWWPQLHSFAIGLKGAPDLIKAREVAEYIGTVHHEINY 300 Query: 301 TVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLY 360 TVQEGLDAIRDVIY IETYDVTT+RASTPMYL++R IK+MGIKMVLSGEG+DEVFGGYLY Sbjct: 301 TVQEGLDAIRDVIYFIETYDVTTVRASTPMYLLARVIKSMGIKMVLSGEGADEVFGGYLY 360 Query: 361 FHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQD 420 FHKAP K+ HEETVRKL LHMYDC RANK++SAWGVE RVPFLDK+FLDVAM +NP+ Sbjct: 361 FHKAPTPKDFHEETVRKLSKLHMYDCLRANKSLSAWGVEGRVPFLDKEFLDVAMALNPKA 420 Query: 421 KMCGNGKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQVSDQQLET 480 KMC ++EK I+RE F LP SVAWRQKEQFSDGVGYSWIDTL+E+ A VSD+Q+E Sbjct: 421 KMCPGKEIEKRIVREAFADMLPESVAWRQKEQFSDGVGYSWIDTLREITAAAVSDEQMEH 480 Query: 481 ARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWDEAFKKMDD 540 A RFP NTP +KE Y YR IFEE FP SAA VP PSVACS+A+A+ WD AF+ +++ Sbjct: 481 AAERFPINTPLNKEEYYYRSIFEEHFPSESAARSVPSVPSVACSTAEALAWDVAFRNLNE 540 Query: 541 PSGRAV-GVHQSAY 553 PSGRAV GVH+ AY Sbjct: 541 PSGRAVRGVHEEAY 554 Lambda K H 0.319 0.135 0.407 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: 935 Number of extensions: 27 Number of successful extensions: 1 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: 554 Length of database: 559 Length adjustment: 36 Effective length of query: 518 Effective length of database: 523 Effective search space: 270914 Effective search space used: 270914 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 350079 BT0551 (asparagine synthetase B [glutamine-hydrolyzing] (NCBI ptt file))
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.12520.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.1e-142 460.1 0.1 2.8e-118 382.0 0.0 2.7 2 lcl|FitnessBrowser__Btheta:350079 BT0551 asparagine synthetase B [ Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:350079 BT0551 asparagine synthetase B [glutamine-hydrolyzing] (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 382.0 0.0 2.8e-118 2.8e-118 1 384 [. 2 371 .. 2 378 .. 0.97 2 ! 76.6 0.1 1.1e-25 1.1e-25 437 517 .] 372 453 .. 368 453 .. 0.96 Alignments for each domain: == domain 1 score: 382.0 bits; conditional E-value: 2.8e-118 TIGR01536 1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.evvivf 75 Cgiagi++ k+++ke ++++ +m+++++hRGPD++g++ ail+h+RL+i+d ++g QPl++ + ++++ + lcl|FitnessBrowser__Btheta:350079 2 CGIAGILNIKTQTKELRDKALKMAQKIRHRGPDWSGIYVG---GSAILAHERLSIVDPQSGGQPLYSPDrKQALAV 74 ***************88********************999...8*************************999**** PP TIGR01536 76 nGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGikPLYya 151 nGEIYNh+++r+++ + y+F+t sD+EViLa+y+ g +++e++ G FAf+l+de+k+e+++aRD++G+ PLY + lcl|FitnessBrowser__Btheta:350079 75 NGEIYNHRDIRARYAGQ-YDFQTGSDCEVILALYKDKGIHFLEEISGIFAFVLYDEEKDEFLIARDPIGVIPLYIG 149 ***************99.********************************************************** PP TIGR01536 152 se.qgkllfaSEiKallalk.eikaeldkealaelltlqlvptektlfkevkelepakaldgeekleeywevekee 225 ++ +gk++f+SE+Kal ++ e +++l+++++ ++ + ++ + +e+ ++e +k++ ++k++ lcl|FitnessBrowser__Btheta:350079 150 KDkDGKIYFGSELKALEGFCnEYEPFLPGHYFYSKEGKM----KRWYTREWTDYESVKDN--DAKVS--------- 210 **99****************99************99998....5799*********9997..44444......... PP TIGR01536 226 vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeak.............sevktFsigfe 288 +++e+ledav+++l++dvp+gvllSGGlDSs+++aiakk+a+ ++++F+ig++ lcl|FitnessBrowser__Btheta:350079 211 ----------DVKEALEDAVHRQLMSDVPYGVLLSGGLDSSVISAIAKKYAAkrietdgasdawwPQLHSFAIGLK 276 ..........5***************************************999************9********** PP TIGR01536 289 dskdldeskaarkvadelgtehkevliseeevlkeleevilale..eptairasiplyllsklarekgvkVvLsGe 362 + +dl ar+va+++gt h+e+ + +e+l+++++vi+ +e ++t++ras+p+yll++ ++ +g+k+vLsGe lcl|FitnessBrowser__Btheta:350079 277 GAPDLI---KAREVAEYIGTVHHEINYTVQEGLDAIRDVIYFIEtyDVTTVRASTPMYLLARVIKSMGIKMVLSGE 349 999999...9****************************************************************** PP TIGR01536 363 GaDElfgGYeyfreakaeeale 384 GaDE+fgGY yf++a+ ++++ lcl|FitnessBrowser__Btheta:350079 350 GADEVFGGYLYFHKAPTPKDFH 371 *****************99998 PP == domain 2 score: 76.6 bits; conditional E-value: 1.1e-25 TIGR01536 437 eellrldlelllsdllrakDrvsmahslEvRvPflDkelvelalsippelklr..dgkeKvlLreaaeellPeeil 510 ee++r+ +l+++d+lra+ + ++a+++E RvPflDke++++a+ ++p++k+ ++ eK++ rea++++lPe+++ lcl|FitnessBrowser__Btheta:350079 372 EETVRKLSKLHMYDCLRAN-KSLSAWGVEGRVPFLDKEFLDVAMALNPKAKMCpgKEIEKRIVREAFADMLPESVA 446 78899999***********.****************************9999888999****************** PP TIGR01536 511 eRkKeaf 517 +R+Ke+f lcl|FitnessBrowser__Btheta:350079 447 WRQKEQF 453 *****99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (517 nodes) Target sequences: 1 (559 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: 0.08u 0.01s 00:00:00.09 Elapsed: 00:00:00.08 # Mc/sec: 3.45 // [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