Align asparagine synthetase B, glutamine-hydrolyzing; EC 6.3.5.4 (characterized)
to candidate 6937968 Sama_2101 asparagine synthetase B (RefSeq)
Query= CharProtDB::CH_002444 (554 letters) >FitnessBrowser__SB2B:6937968 Length = 554 Score = 795 bits (2053), Expect = 0.0 Identities = 388/554 (70%), Positives = 451/554 (81%), Gaps = 1/554 (0%) Query: 1 MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGA 60 MCSIF + DI++DA +R+ ALE+S+L+RHRGPDWSGIYA D+A+LAHERL+IVD+ GA Sbjct: 1 MCSIFAILDIQSDASAMRQVALEMSKLLRHRGPDWSGIYADDHAVLAHERLAIVDIEHGA 60 Query: 61 QPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPEFLDDLQG 120 QPL + + VLAVNGEIYNH+ L+AE GD+Y +QT SDCEVILALYQE G +FLD L G Sbjct: 61 QPLISDDGSLVLAVNGEIYNHKELKAELGDKYSYQTNSDCEVILALYQEYGSDFLDKLNG 120 Query: 121 MFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIKEFPAGSY 180 +FAF LYD K YLIGRDH+GIIPLY G D G YVASEMKALVPVC+T++ F G Y Sbjct: 121 IFAFVLYDKAKGTYLIGRDHIGIIPLYTGRDAKGNFYVASEMKALVPVCKTVETFAPGHY 180 Query: 181 LWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVLLSGGLDS 240 L S D + YY RDW +DAV DN ELR ALE +VK LMSDVPYGVLLSGGLDS Sbjct: 181 LSSTDAQPVRYYQRDWQAFDAVVDNEASVEELRGALEAAVKRQLMSDVPYGVLLSGGLDS 240 Query: 241 SIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTVHHEIHF 300 SI+SAIT+ +A RR+ED + SEAWWPQLHSFAVGL GSPDL A+++VA+ +GT+HHEIHF Sbjct: 241 SIVSAITQTFAKRRIEDNDESEAWWPQLHSFAVGLKGSPDLAASRKVADAIGTIHHEIHF 300 Query: 301 TVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLY 360 T QEGLDAI+DVIYH+ETYDVTTIRA+TPMYLM+RKIKAMGIKMVLSGEG+DE+FGGYLY Sbjct: 301 TFQEGLDAIKDVIYHLETYDVTTIRAATPMYLMARKIKAMGIKMVLSGEGADELFGGYLY 360 Query: 361 FHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQD 420 FHKAPN + HEE VRKL LH++DC RANKAM+AWG+EARVPFLDK+F+DVAMR+NP Sbjct: 361 FHKAPNPQAFHEELVRKLDKLHLFDCLRANKAMAAWGLEARVPFLDKEFMDVAMRLNPAA 420 Query: 421 KMCGNGKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQVSDQQLET 480 KM G GK+EKHILRE FE LPA +AWRQKEQFSDGVGYSWID LKE AA QV D QL Sbjct: 421 KMSGKGKIEKHILREAFEHKLPAEIAWRQKEQFSDGVGYSWIDGLKEQAAAQVDDLQLAN 480 Query: 481 ARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWDEAFKKMDD 540 ARFRFP+NTP +KEAY YR FEELFPL SAA VPGG SVACS+ +A+ WD + + + D Sbjct: 481 ARFRFPHNTPETKEAYFYRCFFEELFPLESAALTVPGGKSVACSTPEALAWDASLQGIID 540 Query: 541 PSGRAV-GVHQSAY 553 PSGRAV VH +Y Sbjct: 541 PSGRAVREVHAQSY 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: 907 Number of extensions: 30 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: 554 Length adjustment: 36 Effective length of query: 518 Effective length of database: 518 Effective search space: 268324 Effective search space used: 268324 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 6937968 Sama_2101 (asparagine synthetase B (RefSeq))
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.20380.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.3e-149 482.6 0.5 7.4e-124 400.5 0.0 2.9 2 lcl|FitnessBrowser__SB2B:6937968 Sama_2101 asparagine synthetase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6937968 Sama_2101 asparagine synthetase B (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 400.5 0.0 7.4e-124 7.4e-124 1 385 [. 2 372 .. 2 382 .. 0.96 2 ! 79.4 0.2 1.4e-26 1.4e-26 437 517 .] 372 453 .. 369 453 .. 0.94 Alignments for each domain: == domain 1 score: 400.5 bits; conditional E-value: 7.4e-124 TIGR01536 1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.evvivfn 76 C+i++i+d + +a+ ++ + em+++l+hRGPD++g++ d ++a+l+h+RLai+d+++gaQPl +++ + v+ +n lcl|FitnessBrowser__SB2B:6937968 2 CSIFAILDIQSDASAMRQVALEMSKLLRHRGPDWSGIYAD---DHAVLAHERLAIVDIEHGAQPLISDDgSLVLAVN 75 ************99999***********************...8************************99******* PP TIGR01536 77 GEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGikPLYyase 153 GEIYNh+eL++el +k y+++t+sD+EViLa+y+e+g +++++L+G FAf+l+d++kg++++ RD++Gi PLY +++ lcl|FitnessBrowser__SB2B:6937968 76 GEIYNHKELKAELGDK-YSYQTNSDCEVILALYQEYGSDFLDKLNGIFAFVLYDKAKGTYLIGRDHIGIIPLYTGRD 151 ****************.************************************************************ PP TIGR01536 154 .qgkllfaSEiKallalk.eikaeldkealaelltlqlvptektlfkevkelepakaldgeekleeywevekeevke 228 +g++++aSE+Kal++++ +++++ ++++l+++ + + ++++++++ ++++ ++ e+ lcl|FitnessBrowser__SB2B:6937968 152 aKGNFYVASEMKALVPVCkTVETFAPGHYLSSTDAQPV----RYYQRDWQAFDAVVDN--EA--------------- 207 9*****************99**********99998885....799*****99999886..33............... PP TIGR01536 229 seeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeak.............sevktFsigfedskd 292 +veelr +le+avk++l++dvp+gvllSGGlDSs+v+ai++ +ak ++++F++g+++s+d lcl|FitnessBrowser__SB2B:6937968 208 ----SVEELRGALEAAVKRQLMSDVPYGVLLSGGLDSSIVSAITQTFAKrriedndeseawwPQLHSFAVGLKGSPD 280 ....4567******************************************************9************** PP TIGR01536 293 ldeskaarkvadelgtehkevliseeevlkeleevilale..eptairasiplyllsklarekgvkVvLsGeGaDEl 367 l a rkvad++gt h+e++++ +e+l+++++vi++le ++t+ira++p+yl++++++++g+k+vLsGeGaDEl lcl|FitnessBrowser__SB2B:6937968 281 LA---ASRKVADAIGTIHHEIHFTFQEGLDAIKDVIYHLEtyDVTTIRAATPMYLMARKIKAMGIKMVLSGEGADEL 354 **...************************************************************************ PP TIGR01536 368 fgGYeyfreakaeealel 385 fgGY yf++a++ +a++ lcl|FitnessBrowser__SB2B:6937968 355 FGGYLYFHKAPNPQAFHE 372 ***************983 PP == domain 2 score: 79.4 bits; conditional E-value: 1.4e-26 TIGR01536 437 eellrldlelllsdllrakDrvsmahslEvRvPflDkelvelalsippelklr..dgkeKvlLreaaeellPeeile 511 eel+r+ +l+l d+lra+ ++++a++lE+RvPflDke++++a++++p +k++ + eK++Lrea+e+ lP ei++ lcl|FitnessBrowser__SB2B:6937968 372 EELVRKLDKLHLFDCLRAN-KAMAAWGLEARVPFLDKEFMDVAMRLNPAAKMSgkGKIEKHILREAFEHKLPAEIAW 447 67788888999********.****************************9999987899******************* PP TIGR01536 512 RkKeaf 517 R+Ke+f lcl|FitnessBrowser__SB2B:6937968 448 RQKEQF 453 ****99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (517 nodes) Target sequences: 1 (554 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: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.08 # Mc/sec: 3.58 // [ok]
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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