Align candidate HSERO_RS21075 HSERO_RS21075 (asparagine synthase)
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.23568.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.4e-127 410.0 0.0 1.3e-126 409.6 0.0 1.2 1 lcl|FitnessBrowser__HerbieS:HSERO_RS21075 HSERO_RS21075 asparagine synthas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS21075 HSERO_RS21075 asparagine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 409.6 0.0 1.3e-126 1.3e-126 1 517 [] 2 562 .. 2 562 .. 0.89 Alignments for each domain: == domain 1 score: 409.6 bits; conditional E-value: 1.3e-126 TIGR01536 1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkde.keenailghrRLaiidlseg.aQPls 66 Cgiag ++++ +++++ +++ l+ ++ RGP+++ ++++ a+lg+ RL++idlse+ QP++ lcl|FitnessBrowser__HerbieS:HSERO_RS21075 2 CGIAGSFWKNSDLQSN-IRMERALQIMRERGPNHQDYHRHDtAGGSALLGQTRLSVIDLSEQaSQPMY 68 ***********99996.56777799***********9999889999**************999***** PP TIGR01536 67 nek.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekk 133 + + ++ ++fnGEIYN+ eLreel ++G +F+t+sDtEV+Laa+e+wge+++ rL+GmFAfa++d + lcl|FitnessBrowser__HerbieS:HSERO_RS21075 69 SPDgRYGLIFNGEIYNYIELREELARAGRNFHTQSDTEVLLAAWEAWGEAALRRLTGMFAFAVFDFQL 136 ******************************************************************** PP TIGR01536 134 gelflaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlq.lvptektlfkev 200 ++ l+RD +GikPL+yas+++ ++faS +a+ al ++l+ + + ++l + ++ ++t+f e lcl|FitnessBrowser__HerbieS:HSERO_RS21075 137 RTCTLVRDAFGIKPLFYASTGEGFYFASDTRAMRALAPCSPALNWQRAYDYLVHGeYDFGNETFFSEF 204 *************************************99*****99999999999999********** PP TIGR01536 201 kelepakal....dgeeklee..ywevekee.vkeseeelveelrelledavkkrlvadvpvgvllSG 261 l+p++ d+++++ +w+ + + ++s+ee+ +lrell ++vk +l++dvp+g+ lSG lcl|FitnessBrowser__HerbieS:HSERO_RS21075 205 SSLSPGHMIevplDQARTMLPrcWWKPSIIKdSTSSFEEASMQLRELLLESVKLHLRSDVPLGAALSG 272 ********987764444444479****998878999******************************** PP TIGR01536 262 GlDSslvaaiakkeak.sevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevi 328 G+DSs++++ +++ + +++tFs +++++e+++ v +++g ++v++++ee++++le +i lcl|FitnessBrowser__HerbieS:HSERO_RS21075 273 GIDSSVIVCAMRQIEPdLPIHTFSFVAS-ESAVSEEHWVDLVNKHVGAIAHKVHVTPEELAHDLESLI 339 ************9998899******999.99************************************* PP TIGR01536 329 laleeptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale............ 384 ++ ep+ ++++ +y ++kla+++gv+V L+G+GaDE++gGY+ + + + l lcl|FitnessBrowser__HerbieS:HSERO_RS21075 340 DTQGEPFGSTSIYAQYRVFKLAQQNGVTVTLDGQGADEMMGGYNGYPGQRMLSLLDkgayvqaltflr 407 ************************************************99999888777666666555 PP TIGR01536 385 ....lpeaselaekkl..................llqaklakeselkellkakleeelkekeelkkel 430 ++ l++ + ++++ + + l+e ++ lcl|FitnessBrowser__HerbieS:HSERO_RS21075 408 nwaaW----------PgrspieglkrlvgagssgQFNSILRRLNGMQNIPDWIRPGPLREAGVRLSYP 465 55440..........03333444444555666656666666666666666666666666655555555 PP TIGR01536 431 kee........seleellrldlelllsdllrakDrvsmahslEvRvPflDkelvelalsippelklr. 489 +++ + ++ l ++ +e+ l +llr Dr sm s+E+RvPfl lve++l+ p e+ ++ lcl|FitnessBrowser__HerbieS:HSERO_RS21075 466 QAQpiapdhgrRMMAFLAQSLTERGLLGLLRHGDRNSMRFSVESRVPFLTTGLVEFMLRQPEEYLVSp 533 555777867755555555666667777888888*********************************** PP TIGR01536 490 dgkeKvlLreaaeellPeeileR.kKeaf 517 +g++K lLr +++++P+++l+R +K +f lcl|FitnessBrowser__HerbieS:HSERO_RS21075 534 SGETKALLRASMRGIVPDAVLDRrDKIGF 562 ***********************999888 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (517 nodes) Target sequences: 1 (627 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: 13.55 // [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